ISMB 2025

This is a list of all sessions at ISMB 2025.

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Showing 729 talks

When?	Room	Speaker	Title	Session	Abstract
14 July 09:00-18:00 (add to calendar)	-		Tutorial VT1: Visualising and interpreting your -omics results using ggplot2 and R	Tutorials	This full-day tutorial introduces participants to the principles of impactful data visualisation and equips them with the skills to create publication [...]
14 July 09:00-13:00 (add to calendar)	-		Tutorial VT6: Beyond Bioinformatics: Snakemake for Versatile Computational Workflows	Tutorials	Snakemake is a powerful, Python-based workflow management system that revolutionises how computational tasks are designed, executed and reproduced. By [...]
14 July 14:00-18:00 (add to calendar)	-		Tutorial VT5: Comprehensive Bioinformatics and Statistical Approaches for High-Throughput Sequencing Data Analysis, Including scRNA-seq, in Biomarker Discovery	Tutorials	With the significant advancements in genomic profiling technologies and the emergence of selective molecular targeted therapies, biomarkers have playe [...]
14 July 14:00-18:00 (add to calendar)	-		Tutorial VT8: Generative AI for Single-Cell Perturbation Modeling: Theoretical and practical considerations	Tutorials	Single-cell perturbation modelling is revolutionising how we understand the effects of genetic interventions, drugs, and cellular stimulants on molecu [...]
15 July 09:00-18:00 (add to calendar)	-		Tutorial VT2: OmicsViz: Interactive Visualization and ML for Omics Data	Tutorials	Data Science and Machine Learning are intricately connected, particularly in computational biology. In a time when biological data is being produced o [...]
15 July 09:00-13:00 (add to calendar)	-		Tutorial VT3: Computational approaches for deciphering cell-cell communication from single-cell transcriptomics and spatial transcriptomics data	Tutorials	Tissues and organs are complex and highly-organized systems composed of diverse cells that work together to maintain homeostasis, drive development an [...]
15 July 09:00-13:00 (add to calendar)	-		Tutorial VT9: Biomedical text mining for knowledge extraction	Tutorials	Modern bioinformatics analyses rely heavily on the existing knowledge of the role of genes and mutations in different diseases, as well as the complex [...]
15 July 14:00-18:00 (add to calendar)	-		Tutorial VT4: An applied genomics approach to crop breeding: A suite of tools for exploring natural and artificial diversity	Tutorials	The urgent need for crop improvement is hindered by the lack of precision in crop breeding. Although significant progress has been made in genomics, m [...]
15 July 14:00-18:00 (add to calendar)	-		Tutorial VT7: Assessing and Enhancing Digital Accessibility of Biological Data and Visualizations	Tutorials	As computational biologists, we produce biological datasets, visualizations, and computational tools. Our shared goal is to make our data and tools wi [...]
20 July 09:00-09:00 (add to calendar)	02N		Student Council Symposium	SCS: Student Council Symposium
20 July 09:00-09:30 (add to calendar)	02N		TBD	SCS: Student Council Symposium
20 July 09:00-10:45 (add to calendar)	11A		Tutorial IP1: Machine Learning for Omics: Best practices and Real-Life Insights with TidyModels	Tutorials	Omics data analysis presents unique challenges due to its high dimensionality and complexity. Supervised machine learning (ML) offers powerful tools f [...]
20 July 09:00-10:45 (add to calendar)	03A		Tutorial IP2: Massively parallel reporter assays in functional regulatory genomics and as part of the IGVF data resource	Tutorials	This tutorial is designed to empower bioinformatics researchers with the knowledge and skills to effectively utilize Massively Parallel Reporter Assay [...]
20 July 09:00-10:45 (add to calendar)	04AB		Tutorial IP3: Genomic Variant Interpretation & prioritisation for clinical research	Tutorials	The interpretation of genetic variation is important for understanding human health and disease. Increased knowledge leads to societal benefits includ [...]
20 July 09:00-10:45 (add to calendar)	03B		Tutorial IP4: Quantum Machine Learning for multi-omics analysis	Tutorials	Single-cell and population-level multi-omics analyses have greatly enhanced our understanding of biological complexity. By integrating various types o [...]
20 July 09:00-10:45 (add to calendar)	12		Tutorial IP5: Introduction to Causal Analysis using Mendelian Randomisation	Tutorials	Mendelian randomisation (MR) is a method that uses genetic variation associated with an exposure (e.g., behaviours, biomarkers) to infer its causal ef [...]
20 July 09:00-10:45 (add to calendar)	11BC		Tutorial IP6: Hello Nextflow: Getting started with workflows for bioinformatics	Tutorials	Nextflow is a powerful and flexible open-source workflow management system that simplifies the development, execution, and scalability of data-driven [...]
20 July 09:30-09:45 (add to calendar)	02N	Mirko Treccani	Nutri-omics: how omics investigation can help designing personalized nutrition research	SCS: Student Council Symposium	(Poly)phenols (PPs) are a group of bioactive compounds found in plant-based food, widely consumed within diet. Several studies have reported the benef [...]
20 July 09:45-10:00 (add to calendar)	02N	Kiran Kumar Eripogu	Nocardia Genomes are a Large Reservoir of Diverse Gene Content, Biosynthetic Gene Clusters, and Species-specific Genes	SCS: Student Council Symposium	Nocardia, an opportunistic pathogenic bacterial genus, remains underexplored in terms of biosynthetic potential, gene content, and evolutionary histor [...]
20 July 10:00-10:05 (add to calendar)	02N	Victor Grentzinger	Lifting the veil on Challenging Medically Relevant Genes	SCS: Student Council Symposium	While the cost of DNA sequencing has never been cheaper, a number of genetic diseases remain difficult to diagnose. Nearly 400 medically relevant gene [...]
20 July 10:05-10:10 (add to calendar)	02N	Alžbeta Rástocká	AccuRate: A Tool Supporting Genotype–Phenotype Analysis and Causal Mutation Discovery in Soybean	SCS: Student Council Symposium	Soybean is one of the world’s most significant crops, serving as an indispensable source of high-quality plant protein and oil for both human and live [...]
20 July 10:10-10:15 (add to calendar)	02N	Ritchie Yu	Early colorectal cancer detection with deep learning on ultra-shallow whole genome sequencing of cell-free DNA	SCS: Student Council Symposium	Early detection of cancer can mitigate adverse patient outcomes by reducing the time to intervention and treatment. Cell-free DNA (cfDNA) circulating [...]
20 July 10:15-10:30 (add to calendar)	02N	Megha Hegde	DNA-DistilBERT: A small language model for non-coding variant effect prediction from human DNA sequences	SCS: Student Council Symposium	Genetic variants have been associated with changes in disease risk. Historically, research has focused on coding variants; however, emerging research [...]
20 July 10:30-10:45 (add to calendar)	02N	Guillermo Prol Castelo	Generative AI for Childhood and Adult Cancer Research	SCS: Student Council Symposium	Cancer is one of the most common causes of death worldwide, and its complexity makes it especially challenging to study. Despite ongoing progress in c [...]
20 July 11:00-11:05 (add to calendar)	02N	Raúl Fernández-Díaz	AutoPeptideML 2: An open source library for democratizing machine learning for peptide bioactivity prediction	SCS: Student Council Symposium	Peptides are a rapidly growing drug modality with diverse bioactivities and accessible synthesis, particularly for canonical peptides composed of the [...]
20 July 11:00-13:00 (add to calendar)	11A		Tutorial IP1: Machine Learning for Omics: Best practices and Real-Life Insights with TidyModels	Tutorials	Omics data analysis presents unique challenges due to its high dimensionality and complexity. Supervised machine learning (ML) offers powerful tools f [...]
20 July 11:00-13:00 (add to calendar)	03A		Tutorial IP2: Massively parallel reporter assays in functional regulatory genomics and as part of the IGVF data resource	Tutorials	This tutorial is designed to empower bioinformatics researchers with the knowledge and skills to effectively utilize Massively Parallel Reporter Assay [...]
20 July 11:00-13:00 (add to calendar)	04AB		Tutorial IP3: Genomic Variant Interpretation & prioritisation for clinical research	Tutorials	The interpretation of genetic variation is important for understanding human health and disease. Increased knowledge leads to societal benefits includ [...]
20 July 11:00-13:00 (add to calendar)	03B		Tutorial IP4: Quantum Machine Learning for multi-omics analysis	Tutorials	Single-cell and population-level multi-omics analyses have greatly enhanced our understanding of biological complexity. By integrating various types o [...]
20 July 11:00-13:00 (add to calendar)	12		Tutorial IP5: Introduction to Causal Analysis using Mendelian Randomisation	Tutorials	Mendelian randomisation (MR) is a method that uses genetic variation associated with an exposure (e.g., behaviours, biomarkers) to infer its causal ef [...]
20 July 11:00-13:00 (add to calendar)	11BC		Tutorial IP6: Hello Nextflow: Getting started with workflows for bioinformatics	Tutorials	Nextflow is a powerful and flexible open-source workflow management system that simplifies the development, execution, and scalability of data-driven [...]
20 July 11:05-11:10 (add to calendar)	02N	Luca Musella	ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and MeSH co-occurrence networks from context-specific biomedical literature	SCS: Student Council Symposium	The accelerating growth of scientific literature overwhelms our capacity to manually distil complex phenomena like molecular networks linked to diseas [...]
20 July 11:15-11:20 (add to calendar)	02N	Muhammed Hunaid Topiwala	TCRBench: A Unified Benchmark for TCR–Antigen Binding Prediction and Clustering	SCS: Student Council Symposium	T-cell receptor (TCR) recognition of antigenic peptides presented by major histocompatibility complex (MHC) molecules is central to adaptive immunity, [...]
20 July 11:20-11:35 (add to calendar)	02N	Hannelore Longin	Fold first, ask later: structure-informed function prediction in Pseudomonas phages	SCS: Student Council Symposium	Phages, the viruses of bacteria, are the most abundant biological entities on earth. In general, phage genomes are densely coded and contain many open [...]
20 July 11:35-11:50 (add to calendar)	02N	Vít Škrhák	Exploring capabilities of protein language models for cryptic binding site prediction	SCS: Student Council Symposium	Identifying protein-ligand binding sites is essential for understanding biological mechanisms and supporting drug discovery. However, accurate predict [...]
20 July 11:50-11:55 (add to calendar)	02N	Nisha Nandhini Shankar	Coarse-grained and Multi-Scale Modeling of Lytic Polysaccharide Monooxygenases: Insights into Family-Specific Dynamics and Protein Frustration	SCS: Student Council Symposium	Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent redox enzymes that catalyze the oxidative cleavage of C1 and/or C4 bonds in recalcitr [...]
20 July 11:55-12:00 (add to calendar)	02N	Małgorzata Drabko	Identification and structural modeling of the novel TTC33-associated core (TANC) complex involved in DNA damage response	SCS: Student Council Symposium	Of the ~20,200 human proteins, ~9% remain functionally uncharacterized, highlighting a gap in our understanding of cell physiology. Structural protein [...]
20 July 12:00-12:05 (add to calendar)	02N	Carla Luciana Padilla Franzotti	Functional Interfaces at Ordered–Disordered Transitions: Conserved Linear Motifs and Flanking Regions in Modular Proteins	SCS: Student Council Symposium	Multidomain proteins integrate ordered domains, structured tandem repeats (STRs), and intrinsically disordered regions (IDRs) to generate modular arch [...]
20 July 12:05-12:10 (add to calendar)	02N	Yitao Eric Sun	Automating Linear Motif Predictions to Map Human Signaling Networks	SCS: Student Council Symposium	Short linear motifs (SLiMs) are critical mediators of transient protein-protein interactions (PPIs), yet only 0.2% of human SLiMs are experimentally v [...]
20 July 12:10-12:25 (add to calendar)	02N	Samuel Davis	Deep Phylogenetic Reconstruction Reveals Key Functional Drivers in the Evolution of B1/B2 Metallo-β-Lactamases	SCS: Student Council Symposium	Metallo-β-lactamases (MBLs) comprise a diverse family of antibiotic-degrading enzymes. Despite their growing implication in drug-resistant pathogens, [...]
20 July 12:25-12:30 (add to calendar)	02N	Ruyi Chen	Multilingual model improves zero-shot prediction of disease effects on proteins	SCS: Student Council Symposium	Models for mutation effect prediction in coding sequences rely on sequence-, structure-, or homology-based features. Here, we introduce a novel method [...]
20 July 12:30-12:45 (add to calendar)	02N	Ana Isabel Castillo Orozco	Integrated analysis of bulk and single-nuclei RNA sequencing data of primary and metastatic pediatric Medulloblastoma.	SCS: Student Council Symposium	Medulloblastoma (MB) is a highly aggressive and the most common brain tumor in childhood. MB presents a high intertumoral heterogeneity, with at least [...]
20 July 12:45-12:50 (add to calendar)	02N	Sara Eslami	Investigating novel transcriptional regulators in symbiotic nodule development of Medicago truncatul	SCS: Student Council Symposium	Biological nitrogen fixation is a crucial process for sustainable agriculture, allowing leguminous plants to convert atmospheric nitrogen into bioavai [...]
20 July 12:50-12:55 (add to calendar)	02N	Vennila Kanchana Devi Marimuthu	Meta-Analysis of Bovine Transcriptome Reveals Key Immune Gene Profiles and Signaling Pathways	SCS: Student Council Symposium	Understanding immune mechanisms in cattle is crucial for improving disease resistance through informed breeding decision and development. Meta-analysi [...]
20 July 12:55-13:00 (add to calendar)	02N	Sachendra Kumar	Post-translational regulation of stemness under DNA damage response contributes to the gingivobuccal oral squamous cell carcinoma relapse and progression	SCS: Student Council Symposium	Tobacco consumption (smoking and particularly smokeless form) contributes to a high prevalence of gingivobuccal oral squamous cell carcinoma (OSCC-GB) [...]
20 July 13:00-17:00 (add to calendar)	-		Youth Bioinformatics Symposium	Special Track
20 July 14:00-15:00 (add to calendar)	02N		TBD	SCS: Student Council Symposium
20 July 14:00-16:00 (add to calendar)	11BC		Tutorial IP7: AI large cellular models and in-silico perturbation	Tutorials	Transformer-based large language models (LLMs) are changing the world. The capabilities they illustrated in sophisticated natural language, vision and [...]
20 July 14:00-16:00 (add to calendar)	12		Tutorial IP8: Representation Learning and Feature Engineering for Genomic Sequences Analysis	Tutorials	Machine learning (ML) has been successfully applied in different omics problems, such as sequence classification in the field of genomics. The effecti [...]
20 July 14:00-16:00 (add to calendar)	11A		Tutorial IP1: Machine Learning for Omics: Best practices and Real-Life Insights with TidyModels	Tutorials	Omics data analysis presents unique challenges due to its high dimensionality and complexity. Supervised machine learning (ML) offers powerful tools f [...]
20 July 14:00-16:00 (add to calendar)	03A		Tutorial IP2: Massively parallel reporter assays in functional regulatory genomics and as part of the IGVF data resource	Tutorials	This tutorial is designed to empower bioinformatics researchers with the knowledge and skills to effectively utilize Massively Parallel Reporter Assay [...]
20 July 14:00-16:00 (add to calendar)	04AB		Tutorial IP3: Genomic Variant Interpretation & prioritisation for clinical research	Tutorials	The interpretation of genetic variation is important for understanding human health and disease. Increased knowledge leads to societal benefits includ [...]
20 July 14:00-16:00 (add to calendar)	03B		Tutorial IP4: Quantum Machine Learning for multi-omics analysis	Tutorials	Single-cell and population-level multi-omics analyses have greatly enhanced our understanding of biological complexity. By integrating various types o [...]
20 July 14:00-16:00 (add to calendar)	02F		Youth Bioinformatics Symposium	Youth Bioinformatics Symposium
20 July 15:00-15:20 (add to calendar)	-		Critical assessment and AI	Fellows Presentation	The abstract for this presentation will be shared by the presenter shortly [...]
20 July 15:00-15:45 (add to calendar)	02N		Bioinformatics at the Heart of Biology.	SCS: Student Council Symposium	This is a career talk for the Student Council [...]
20 July 15:20-15:40 (add to calendar)	-	Julio Saez-Rodriguez	Rethinking Rigor: Benchmarking in the Age of Foundation Models	Fellows Presentation	The abstract for this presentation will be shared by the presenter shortly [...]
20 July 15:30-18:00 (add to calendar)	-		Fellows Workshop	Special Track
20 July 15:40-15:50 (add to calendar)	-		Break	Fellows Presentation
20 July 15:45-16:00 (add to calendar)	02N		Closing remarks	SCS: Student Council Symposium
20 July 15:50-16:10 (add to calendar)	-	Robert Murphy	One Foundation Model to Rule Them All?	Fellows Presentation	The abstract for this presentation will be shared by the presenter shortly [...]
20 July 16:00-18:00 (add to calendar)	-		Career Fair	Special Track
20 July 16:10-16:40 (add to calendar)	-		Gaps in the capabilities of generative AI systems; ISCB's role in promoting international research and educational collaborations	Fellows Presentation	The abstract for this presentation will be shared by the presenter shortly [...]
20 July 16:15-18:00 (add to calendar)	11BC		Tutorial IP7: AI large cellular models and in-silico perturbation	Tutorials	Transformer-based large language models (LLMs) are changing the world. The capabilities they illustrated in sophisticated natural language, vision and [...]
20 July 16:15-18:00 (add to calendar)	12		Tutorial IP8: Representation Learning and Feature Engineering for Genomic Sequences Analysis	Tutorials	Machine learning (ML) has been successfully applied in different omics problems, such as sequence classification in the field of genomics. The effecti [...]
20 July 16:15-18:00 (add to calendar)	11A		Tutorial IP1: Machine Learning for Omics: Best practices and Real-Life Insights with TidyModels	Tutorials	Omics data analysis presents unique challenges due to its high dimensionality and complexity. Supervised machine learning (ML) offers powerful tools f [...]
20 July 16:15-18:00 (add to calendar)	03A		Tutorial IP2: Massively parallel reporter assays in functional regulatory genomics and as part of the IGVF data resource	Tutorials	This tutorial is designed to empower bioinformatics researchers with the knowledge and skills to effectively utilize Massively Parallel Reporter Assay [...]
20 July 16:15-18:00 (add to calendar)	04AB		Tutorial IP3: Genomic Variant Interpretation & prioritisation for clinical research	Tutorials	The interpretation of genetic variation is important for understanding human health and disease. Increased knowledge leads to societal benefits includ [...]
20 July 16:15-18:00 (add to calendar)	03B		Tutorial IP4: Quantum Machine Learning for multi-omics analysis	Tutorials	Single-cell and population-level multi-omics analyses have greatly enhanced our understanding of biological complexity. By integrating various types o [...]
20 July 16:15-18:00 (add to calendar)	02F		Youth Bioinformatics Symposium	Youth Bioinformatics Symposium
20 July 16:40-17:10 (add to calendar)	-		Discussion	Fellows Presentation
20 July 18:30-19:30 (add to calendar)	01A	John Jumper	Extending AlphaFold to make predictions across the universe of biomolecular interactions	Distinguished Keynotes	The high accuracy of AlphaFold 2 in predicting protein structures and protein-protein interactions raises the question of how to extend the success of [...]
21 July 08:40-09:00 (add to calendar)	01A	-	Morning Welcome and Keynote Introduction	Distinguished Keynotes
21 July 09:00-10:00 (add to calendar)	01A	Amos Bairoch	Plus ça change, plus c'est la même chose	Distinguished Keynotes	Amos Bairoch will reflect on 40 years of biocuration, from Swiss-Prot to Cellosaurus, highlighting how core challenges and values have endured despite [...]
21 July 11:20-12:00 (add to calendar)	03B	Franca Fraternali	Decoding Immunity: Structural and Dynamical Insights Driving Antibody Innovation	3DSIG: Structural Bioinformatics and Computational Biophysics	Effective adaptive immune responses rely on antibodies of different isotypes performing distinct effector functions. Understanding their structural di [...]
21 July 11:20-11:30 (add to calendar)	03A		Opening Remarks	BOSC: Bioinformatics Open Source Conference
21 July 11:20-12:00 (add to calendar)	01B	Paul Kersey	Molecular Digitisation and Biodiversity Bioinformatics	Bioinformatics in the UK	Biological collections (such as herbarium and fungarium specimens) are the prescurors of modern biobanks; the defining types of taxonomic concepts; to [...]
21 July 11:20-11:40 (add to calendar)	11A	Cenk Sahinalp	Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer	EvolCompGen: Evolution & Comparative Genomics	In the era of precision medicine, performing comparative analysis over diverse patient populations is a fundamental step towards tailoring healthcare [...]
21 July 11:20-11:40 (add to calendar)	02N	Witold Dyrka	Harnessing Deep Learning for Proteome-Scale Detection of Amyloid Signaling Motifs	GenCompBio: General Computational Biology	Amyloid signaling sequences adopt the cross-β fold that is capable of self-replication in the templating process. Propagation of the amxyloid fold fro [...]
21 July 11:20-12:20 (add to calendar)	01A	Julien Gagneur	Where does it hurt (in your genome)?	MLCSB: Machine Learning in Computational and Systems Biology	The identification of genetic variants strongly affecting when phenotypes remains an unsolved problem with major relevance in rare diseases diagnostic [...]
21 July 11:20-11:40 (add to calendar)	02F		Opening Remarks for NIH Track	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing
21 July 11:20-11:22 (add to calendar)	12		Welcome and Introductions	Publications - Navigating Journal Submissions
21 July 11:20-11:40 (add to calendar)	11BC	Daniel Rice	UniProt: Evolving Tools and Data for Protein Science	Tech Track	The Universal Protein Resource (UniProt) is a cornerstone of molecular biology and bioinformatics, delivering high-quality, freely accessible protein [...]
21 July 11:20-12:00 (add to calendar)	04AB	Alexander Sasse	Enhancing Multi-Task CNNs for Regulatory Genomics Through Allelic and High-Resolution Training	VarI: Variant Interpretation	Multi-task Convolutional Neural Networks (CNNs) have emerged as powerful tools for deciphering how genomic sequence determines gene regulatory respons [...]
21 July 11:22-11:40 (add to calendar)	12	Thomas Lengauer	Effective cover letter writing and manuscript preparation for submitting manuscripts in crowded research areas	Publications - Navigating Journal Submissions	I am one of the two Editors-in-Chief of the ISCB Society Journal Bioinformatics Advances that is published jointly with Oxford University Press. After [...]
21 July 11:30-11:35 (add to calendar)	03A		Open Bioinformatics Foundation update	BOSC: Bioinformatics Open Source Conference
21 July 11:35-11:40 (add to calendar)	03A		Tribute to Peter Amstutz	BOSC: Bioinformatics Open Source Conference
21 July 11:40-12:40 (add to calendar)	03A	Christine Orengo	Working together to develop, promote and protect our data resources: Lessons learnt developing CATH and TED	BOSC: Bioinformatics Open Source Conference	The CATH protein domain structure classification was the vision of the pioneering computational scientist Janet Thornton. Algorithms developed by Oren [...]
21 July 11:40-12:00 (add to calendar)	11A	Henri Schmidt	Fast tumor phylogeny regression via tree-structured dual dynamic programming	EvolCompGen: Evolution & Comparative Genomics	Reconstructing the evolutionary history of tumors from bulk DNA sequencing of multiple tissue samples remains a challenging computational problem, req [...]
21 July 11:40-12:00 (add to calendar)	02N	Bingxin Zhou	From High-Throughput Evaluation to Wet-Lab Studies: Advancing Mutation Effect Prediction with a Retrieval-Enhanced Model	GenCompBio: General Computational Biology	Enzyme engineering is a critical approach for producing enzymes that meet industrial and research demands by modifying wild-type proteins to enhance p [...]
21 July 11:40-12:00 (add to calendar)	02F	Liang Dong	Graph Kolmogorov-Arnold Networks for Interpretable Alzheimer's Disease Diagnosis from Structural MRI	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that poses significant diagnostic challenges due to its complex etiology. Graph C [...]
21 July 11:40-11:50 (add to calendar)	12	Laura Mesquita	Choosing journals for submission in popular topics	Publications - Navigating Journal Submissions	There are many factors that authors may take into account when submitting to a journal: scope fit, journal metrics, speed, names on the editorial boar [...]
21 July 11:40-12:20 (add to calendar)	11BC		Genomics 2 Proteins portal: A resource and discovery platform for linking genetic screening outputs to protein sequences and structures	Tech Track	Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional geno [...]
21 July 11:50-12:00 (add to calendar)	12	Feilim Mac Gabhann	How editors make decisions on submissions?	Publications - Navigating Journal Submissions
21 July 12:00-12:20 (add to calendar)	03B	Meghana Kshirsagar	Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm	3DSIG: Structural Bioinformatics and Computational Biophysics	The majority of proteins must form higher-order assemblies to perform their biological functions, yet few machine learning models can accurately and r [...]
21 July 12:00-12:20 (add to calendar)	01B	Arne De Klerk	KnetMiner for Smarter Science: Leveraging Knowledge Graphs & LLMs for Productive Gene Research	Bioinformatics in the UK	In the interpretation of high‑throughput genomic data, the identification of candidate genes underlying differential expression or genome‑wide associa [...]
21 July 12:00-12:20 (add to calendar)	11A	Xiang Ge Luo	Bayesian inference of fitness landscapes via tree-structured branching processes	EvolCompGen: Evolution & Comparative Genomics	Motivation: The complex dynamics of cancer evolution, driven by mutation and selection, underlies the molecular heterogeneity observed in tumors. The [...]
21 July 12:00-12:20 (add to calendar)	02N	Yoochan Myung	BE3D: A Computational Workflow for Integrative Structure-Function Analysis of Base-Editor Tiling Mutagenesis Data	GenCompBio: General Computational Biology	Understanding functional consequences of single-nucleotide variants is critical for elucidating the genetic basis of diseases, yet current variant scr [...]
21 July 12:00-12:20 (add to calendar)	02F		Network Science for Cyber-physical Twinning of Human Heart	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing
21 July 12:00-12:10 (add to calendar)	12	Michael J E Sternberg	How do editors decide on accepting papers on highly similar topics?	Publications - Navigating Journal Submissions	I will base my talk on my experience of being an Editor for Journal of Molecular Biology focussing on computational biology. In particular, every year [...]
21 July 12:00-12:20 (add to calendar)	04AB	Lindsey Plenderleith	Combining massively parallel reporter assays and graph genomics to assay the regulatory effects of indels and structural variants	VarI: Variant Interpretation	Many important phenotypes are driven by differences in gene expression caused by variation in regulatory sequences between individuals. Among such var [...]
21 July 12:10-12:20 (add to calendar)	12	Michael Markie	How and why eLife selects papers for peer review	Publications - Navigating Journal Submissions	eLife is working to promote a culture in which the actual content of a paper is more important than the name of the journal in which it is published. [...]
21 July 12:20-12:40 (add to calendar)	03B	Zhidian Zhang	Probing Homo-Oligomeric Interaction Signals in Protein Language Models	3DSIG: Structural Bioinformatics and Computational Biophysics	Homo-oligomeric protein complexes—assemblies of identical subunits—are central to many biological processes and disease mechanisms. Accurate predictio [...]
21 July 12:20-12:40 (add to calendar)	01B	Ellen Cameron	Lichen Cell Atlas: Tools for exploring photosymbiotic associations	Bioinformatics in the UK	Photosymbiotic associations are partnerships where one partner is photosynthetic, termed the photobiont. Such associations span the eukaryotic tree of [...]
21 July 12:20-12:40 (add to calendar)	11A	Emilia Hurtado	MiClone: A Probabilistic Method for Inferring Cell Phylogenies from Mitochondrial Variants	EvolCompGen: Evolution & Comparative Genomics	Cancer development and progression is largely fuelled by somatic mutations that give rise to clones – distinct subpopulations of malignant cells that [...]
21 July 12:20-12:40 (add to calendar)	02N	Yunjia Li	Enhanced protein evolution with inverse folding models using structural and evolutionary constraints	GenCompBio: General Computational Biology	Protein engineering enables artificial protein evolution through iterative sequence changes, but current methods often suffer from low success rates a [...]
21 July 12:20-12:40 (add to calendar)	01A	Minh Hoang	Locality-aware pooling enhances protein language model performance across varied applications	MLCSB: Machine Learning in Computational and Systems Biology	Protein language models (PLMs) are amongst the most exciting recent advances for characterizing protein sequences, and have enabled a diverse set of a [...]
21 July 12:20-12:40 (add to calendar)	02F	Honggang Wang	A Digital Twins Prototype for Monitoring and Predicting Dynamic Diet-related Health Conditions	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	A digital twin system aims to create a virtual representation of a physical subject by modeling both its intrinsic attributes and the external factors [...]
21 July 12:20-12:55 (add to calendar)	12		Panel Discussion	Publications - Navigating Journal Submissions
21 July 12:20-12:40 (add to calendar)	11BC	Patrick Gohl	ModCRE: modelling protein–DNA interactions and transcription-factor co-operativity in cis-regulatory elements	Tech Track	ModCRE is a web server using a structural approach to predict Transcription Factor binding preferences and auto-mate modelling of higher order regulat [...]
21 July 12:20-12:30 (add to calendar)	04AB	Ruyi Chen	Multilingual model improves zero-shot prediction of disease effects on proteins	VarI: Variant Interpretation	Models for mutation effect prediction in coding sequences rely on sequence-, structure-, or homology-based features. Here, we introduce a novel method [...]
21 July 12:30-12:40 (add to calendar)	04AB	Marco Anteghini	X-MAP: Explainable AI Platform for Genetic Variant Interpretation	VarI: Variant Interpretation	Genetic variants, particularly missense mutations, can significantly affect protein function and contribute to disease development. Methods like CADD [...]
21 July 12:40-13:00 (add to calendar)	03B	Petr Popov	OrgNet: Orientation-gnostic protein stability assessment using convolutional neural networks.	3DSIG: Structural Bioinformatics and Computational Biophysics	Accurately predicting the impact of single-point mutations on protein stability is crucial for elucidating molecular mechanisms underlying diseases in [...]
21 July 12:40-13:00 (add to calendar)	03A	Serghei Mangul	Analytical code sharing practices in biomedical research	BOSC: Bioinformatics Open Source Conference	Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. [...]
21 July 12:40-13:00 (add to calendar)	03A	Seun Olufemi	Connecting Data, People, and Purpose: How Open Science is Advancing Bioinformatics in a Low-Resource region (Nigeria)	BOSC: Bioinformatics Open Source Conference	In many low-resource regions, access to scientific training, collaboration opportunities, and computational tools remains limited, hindering both loca [...]
21 July 12:40-13:00 (add to calendar)	03A	Bhavesh Patel	Introducing the Actionable Guidelines for FAIR Research Software Task Force	BOSC: Bioinformatics Open Source Conference	The Research Software Alliance (ReSA) has established a Task Force dedicated to translating the FAIR principles for Research Software (FAIR4RS Princip [...]
21 July 12:40-13:00 (add to calendar)	01B	Laura-Jayne Gardiner	How can emerging AI technologies benefit multi-omic analysis for crop and soil sustainability	Bioinformatics in the UK	The field of AI is rapidly evolving. At IBM Research (UK), our work in molecular biology has developed from a focus on bioinformatics and computationa [...]
21 July 12:40-12:50 (add to calendar)	11A	Jonghyun Lee	scVarID: Mapping Genetic Variants at Single-Cell Resolution to Uncover Precursor Cells in Cancer	EvolCompGen: Evolution & Comparative Genomics	Next-generation sequencing technologies enable the identification of genetic variants and gene expression; however, measuring both features simultaneo [...]
21 July 12:40-13:00 (add to calendar)	02N	Siyuan Shen	Precise Prediction of Hotspot Residues in Protein-RNA Complexes Using Graph Attention Networks and Pre-trained Protein Language Models	GenCompBio: General Computational Biology	Motivation: Protein-RNA interactions play a pivotal role in biological processes and disease mechanisms, with hotspot residues being critical for targ [...]
21 July 12:40-13:00 (add to calendar)	01A	Daniel Olson	NEAR: Neural Embeddings for Amino acid Relationships	MLCSB: Machine Learning in Computational and Systems Biology	Protein language models (PLMs) have recently demonstrated potential to supplant classical protein database search methods based on sequence alignment, [...]
21 July 12:40-13:00 (add to calendar)	02F	Matthew F. Singh	Multiscale Digital-Twin Modeling and Estimation with Indirect, Neurological Data	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	Linking data and predictions across spatial scales has been a key hurdle to digital twin applications in medicine. Noninvasive measurements, such as e [...]
21 July 12:40-12:50 (add to calendar)	04AB	Alexander Gress	StructGuy: Data leakage free prediction of functional effects of genetic variants.	VarI: Variant Interpretation	In recent years, machine learning models for predicting variant effects on protein function have been dominated by unsupervised models doing zero-shot [...]
21 July 12:50-13:00 (add to calendar)	11A	Aisha	High-Resolution Discovery of Lineage-Specific SVs in Pan Genus Through Assembly Comparisons	EvolCompGen: Evolution & Comparative Genomics	The two sister species in the Pan genus, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus), exhibit lineage-specific differences for several be [...]
21 July 12:50-13:00 (add to calendar)	04AB	Kilian Salomon	Functional characterization of standing variation around disease-associated genes using Massively Parallel Reporter Assays	VarI: Variant Interpretation	A substantial reservoir of disease-associated variants resides in non-coding sequences, particularly in proximal and distal gene regulatory sequences. [...]
21 July 13:00-14:00 (add to calendar)	-		Bioinfo4Women Meet-Up: Supporting Women in Bioinformatics	Bioinfo4Women Meet-Up	Women are still underrepresented in science, particularly at senior career levels and leadership. The "leaky pipeline" persists in bioinformatics, as [...]
21 July 14:00-14:40 (add to calendar)	03B	Adrian Mulholland	Simulations in the age of AlphaFold: dynamics, drug resistance and enzyme design	3DSIG: Structural Bioinformatics and Computational Biophysics	Molecular simulations contribute to practical protein design and engineering workflows. Equilibrium molecular dynamics (MD) simulations not only test [...]
21 July 14:00-14:20 (add to calendar)	03A	Su Datt Lam	AMRColab: An Open-Access, Modular Bioinformatics Suite for Accessible Antimicrobial Resistance Genome Analysis	BOSC: Bioinformatics Open Source Conference	Antimicrobial resistance (AMR) is a global health crisis, projected to cause 39 million deaths by 2050. Surveillance of AMR pathogens is essential for [...]
21 July 14:00-14:20 (add to calendar)	03A	Fabian Woller	NApy: Efficient Statistics in Python for Large-Scale Heterogeneous Data with Enhanced Support for Missing Data	BOSC: Bioinformatics Open Source Conference	Existing Python libraries and tools lack the ability to efficiently run statistical test (such as Pearson correlation, ANOVA, Mann-Whitney-U test) for [...]
21 July 14:00-14:20 (add to calendar)	03A	Peter Cock	pyANI-plus -- whole-genome classification of microbes using Average Nucleotide Identity and similar methods	BOSC: Bioinformatics Open Source Conference	pyANI-plus is an open source MIT licensed Python tool for whole-genome classification of microbes using Average Nucleotide Identity (ANI) and similar [...]
21 July 14:00-14:20 (add to calendar)	01B	Iain Buchan	Civic Data-Driven Innovation for Global Health and AI for All	Bioinformatics in the UK	Professor Buchan will explore how some of the world’s most pressing public health challenges might best be tackled with a global network of learning h [...]
21 July 14:00-14:15 (add to calendar)	12	Julio Saez-Rodriguez	Benchmarking foundation models in biology: where we are, and we where we want to go with the community	DREAM Challenges	The AI promise of powerful solutions to solve biomedical and healthcare related problems needs to be accompanied by a transparent evaluation and proof [...]
21 July 14:00-14:20 (add to calendar)	11BC	Irene Julca	Tracing the functional divergence of duplicated genes	EvolCompGen: Evolution & Comparative Genomics	Gene duplication is a fundamental driver of functional innovation in evolution. Following duplication, paralogous genes may be retained, diverge in fu [...]
21 July 14:00-14:20 (add to calendar)	02N	Jin Zhang	Trustworthy Causal Biomarker Discovery: A Multiomics Brain Imaging Genetics based Approach	GenCompBio: General Computational Biology	Discovering genetic variations underpinning brain disorders is important to understand their pathogenesis. Indirect associations or spurious causal re [...]
21 July 14:00-14:05 (add to calendar)	01C		Welcome Address	ISCB-China Workshop
21 July 14:00-14:20 (add to calendar)	01A	Gianluca Lombardi	LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences	MLCSB: Machine Learning in Computational and Systems Biology	Intrinsic disorder regions (IDR) and soft disorder regions (SDR) provide crucial information on a protein structure to underpin its functioning, inter [...]
21 July 14:00-14:20 (add to calendar)	02F		Advancing Discovery through GenAI and Scalable Infrastructure	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	Opening remarks from the NIH Center for Information Technology (CIT) will highlight how the STRIDES Initiative and Cloud Lab program are accelerating [...]
21 July 14:00-14:20 (add to calendar)	11A	Tuomas Borman	Orchestrating Microbiome Analysis with Bioconductor	Tech Track	Microbes play a crucial role in human health, disease, and the environment. Despite their significant impact, the mechanisms underlying microbiome int [...]
21 July 14:00-14:40 (add to calendar)	04AB	Ellen McDonagh	Variant Interpretation at Scale, for safer and more effective disease treatment	VarI: Variant Interpretation
21 July 14:05-14:30 (add to calendar)	01C	Hongyu Zhao	Modeling and predicting single-cell multi-gene perturbation responses	ISCB-China Workshop	Understanding cellular responses to genetic perturbations is essential for deciphering gene regulation and phenotype formation. While high-throughput [...]
21 July 14:15-14:45 (add to calendar)	12		Building Foundation Models for Single-cell Omics and Imaging	DREAM Challenges	Keynote: This talk delves into the innovative utilization of generative AI in propelling biomedical research forward. By harnessing single-cellsequenc [...]
21 July 14:20-14:40 (add to calendar)	03A	Matthias Blum	InterProScan 6: a modern large-scale protein function annotation pipeline	BOSC: Bioinformatics Open Source Conference	InterProScan 6 represents a major step forward in protein function annotation, addressing the scalability, modularity, and usability limitations of it [...]
21 July 14:20-14:30 (add to calendar)	01B	Emily Jefferson	Health data organisation and landscape across the UK	Bioinformatics in the UK	Professor Jefferson will explore the key challenges and opportunities in the field of clinical and health data science. Drawing on her transition from [...]
21 July 14:20-14:40 (add to calendar)	11BC	Agnieszka Mykowiecka	Duplication Episode Clustering in Phylogenetic Networks	EvolCompGen: Evolution & Comparative Genomics	Phylogenetic networks provide a powerful framework for representing complex evolutionary histories that traditional tree-based models cannot adequatel [...]
21 July 14:20-14:40 (add to calendar)	03A	Ian Gingerich	Randomized Spatial PCA (RASP): a computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data	GenCompBio: General Computational Biology	Spatial transcriptomics (ST) provides critical insights into the complex spatial organization of gene expression in tissues, enabling researchers to u [...]
21 July 14:20-14:40 (add to calendar)	01A	Se Yeon Seo	TCR-epiDiff: Solving Dual Challenges of TCR Generation and Binding Prediction	MLCSB: Machine Learning in Computational and Systems Biology	Motivation: T-cell receptors (TCRs) are fundamental components of the adaptive immune system, recognizing specific antigens for targeted immune respon [...]
21 July 14:20-14:40 (add to calendar)	02F	Kristi Holmes	A Global Model for FAIR and Open Research: Scalable, Collaborative Infrastructure in Action	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	Learn how Zenodo and InvenioRDM are advancing global biomedical research through scalable, AI-integrated, and FAIR-aligned infrastructure. This sessio [...]
21 July 14:20-14:40 (add to calendar)	11A		Smart Turkana Beads: A Culturally Embedded IoT Innovation for Health Monitoring and Drug Adherence	Tech Track	Access to quality healthcare remains a persistent challenge in marginalized regions such as Turkana County in northern Kenya, where traditional belie [...]
21 July 14:30-15:00 (add to calendar)	01B	Angela Wood	The COALESCE study	Bioinformatics in the UK	Professor Wood will present a flagship health data research programme, showcasing how national-scale data assets and analytical infrastructure have en [...]
21 July 14:30-14:50 (add to calendar)	01C	Kai Ye	Seq2Image: Computational Paradigm and Genomic Applications	ISCB-China Workshop	Seq2Image is a computational framework that transforms sequential biological data (e.g., DNA, RNA, protein sequences) into structured 2D image represe [...]
21 July 14:40-15:00 (add to calendar)	03B	Ali Baran Taşdemir	FlowProt: Classifier-Guided Flow Matching for Targeted Protein Backbone Generation in the de novo DNA Methyltransfarase Family	3DSIG: Structural Bioinformatics and Computational Biophysics	Designing novel proteins with both structural stability and targeted molecular function remains a central challenge in computational biology. While re [...]
21 July 14:40-15:00 (add to calendar)	03A	Suneth Samarasinghe	Real-time base modification analysis for nanopore sequencing	BOSC: Bioinformatics Open Source Conference	Real-time analysis of DNA base modifications, particularly methylation, is crucial for making rapid decisions in contexts such as forensics and clinic [...]
21 July 14:40-15:00 (add to calendar)	03A	Bonson Wong	Open-Source GPU Acceleration for State-of-the-Art Nanopore Basecalling with Slorado	BOSC: Bioinformatics Open Source Conference	Nanopore sequencing has become a popular technology for genomic research because of its cost-effectiveness and ability to sequence long reads. Nanopor [...]
21 July 14:40-15:00 (add to calendar)	03A	Sinisa Ivkovic	Voyager-SDK: integrating and automating pipeline runs using Voyager-SDK and Voyager platform	BOSC: Bioinformatics Open Source Conference	At Memorial Sloan Kettering Cancer Center (MSKCC), we developed Voyager, a platform to automate the execution of computational pipelines built using c [...]
21 July 14:40-15:00 (add to calendar)	11BC	Katyayni Ganesan	PhytClust: Accurate and Fast Clustering in Phylogenetic Trees	EvolCompGen: Evolution & Comparative Genomics	Phylogenetic trees serve an important role in disentangling the evolutionary relationships between taxa, across diverse fields. A key question is the [...]
21 July 14:40-15:00 (add to calendar)	02N	Hadasa Kaufman	Genetic Confounding and Comorbidity: Re-evaluating Causal Inference in Disease Associations	GenCompBio: General Computational Biology	Comorbidity analyses indicate that ~35% of common disease pairs tend to occur sequentially within the same individual. Understanding whether this como [...]
21 July 14:40-15:00 (add to calendar)	01A	Chau Do	Incorporating Hierarchical Information into Multiple Instance Learning for Patient Phenotype Prediction with scRNA-seq Data	MLCSB: Machine Learning in Computational and Systems Biology	Multiple Instance Learning (MIL) provides a structured approach to patient phenotype prediction with single-cell RNA-sequencing (scRNA-seq) data. Howe [...]
21 July 14:40-15:00 (add to calendar)	02F	Luca Foschini	Beyond Data Sharing: AI-Powered Solutions for Effective Biomedical Data Reuse	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	This session will showcase AI-powered innovations that move biomedical research beyond data sharing toward meaningful data reuse. Using real-world pla [...]
21 July 14:40-15:00 (add to calendar)	11A		Integrating Long-Read Sequencing and Multiomics for Precision Cell Line Engineering	Tech Track	Optimizing the biomanufacturing of therapeutic molecules, such as monoclonal antibodies, is critical for delivering efficient and scalable patient tre [...]
21 July 14:40-15:00 (add to calendar)	04AB	Thomas Renne	scFunBurd: Quantifying the cellular liability for complex disorders of all rare gene-disrupting variants.	VarI: Variant Interpretation	Neurodevelopmental disorders are examples of complex disorders with multidimensional etiologies. This study focuses on Autism Spectrum Disorder (ASD), [...]
21 July 14:45-15:00 (add to calendar)	12	Maria Brbic	Predicting Perturbation Effects: Are We Really There?	DREAM Challenges	TBA [...]
21 July 14:50-15:10 (add to calendar)	01C	Liang Huang	Language AI for Viruses, Vaccines, and Drugs	ISCB-China Workshop	This talk highlights some highly unexpected connections between biology and linguistics. For example, our Nature (2023) paper designed highly stable a [...]
21 July 15:00-15:20 (add to calendar)	03B	Remo Rohs	Molecular design and structure-based modeling with generative deep learning	3DSIG: Structural Bioinformatics and Computational Biophysics	The rapid expansion of crystal structure data and libraries of readily synthesizable molecules has recently opened up new areas of chemical space for [...]
21 July 15:00-15:20 (add to calendar)	03A	Jose Espinosa-Carrasco	Empowering Bioinformatics Communities with nf-core: The success of an open-source bioinformatics ecosystem	BOSC: Bioinformatics Open Source Conference	The nf-core community exemplifies how open-source software development fosters collaboration, innovation, and sustainability in bioinformatics. nf-cor [...]
21 July 15:00-15:20 (add to calendar)	01B	Tim Beck	TRE-FX platform for federated analytics of sensitive data in Trusted Research Environments	Bioinformatics in the UK	A Trusted Research Environment (TRE) is a highly secure computer system that allows sensitive data from different sources to be combined, de-personali [...]
21 July 15:00-15:15 (add to calendar)	12	Pablo Meyer-Rojas	AI Alliance: Benchmarking foundation models for drug discovery	DREAM Challenges	The AI Alliance is focused on fostering an open community and enabling developers and researchers to accelerate responsible innovation in AI while ens [...]
21 July 15:00-15:20 (add to calendar)	11BC	Ruyi Chen	Learning the Language of Phylogeny with MSA Transformer	EvolCompGen: Evolution & Comparative Genomics	Classical phylogenetic inference assumes independence between sites, potentially undermining the accuracy of evolutionary analyses in the presence of [...]
21 July 15:00-15:20 (add to calendar)	02N	Julian Stamp	Sparse modeling of interactions enables fast detection of genome-wide epistasis in biobank-scale studies	GenCompBio: General Computational Biology	The lack of computational methods capable of detecting epistasis in biobanks has led to uncertainty about the role of non-additive genetic effects on [...]
21 July 15:00-15:10 (add to calendar)	01A	Julián García-Vinuesa	PANDORA: Peptide-based ANtimicrobial Design Optimized by Reinforcement Automation	MLCSB: Machine Learning in Computational and Systems Biology	The global rise of antibiotic resistance, particularly in critical pathogens such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter [...]
21 July 15:00-15:20 (add to calendar)	02F	Tanja Davidsen	Reusable Cyberinfrastructure and Use Cases for the Cancer Research Data Commons (CRDC)	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	This session highlights how NIH’s Cancer Research Data Commons (CRDC) and supporting cyberinfrastructure are transforming cancer research through scal [...]
21 July 15:00-15:20 (add to calendar)	11A	Harry Allsopp	Lonza Sponsor Talk	Tech Track
21 July 15:00-15:20 (add to calendar)	04AB	Magdalena Strauss	Biostatistical approaches to single-cell perturbation screens to create a prospective map of mutational impact	VarI: Variant Interpretation	DNA single nucleotide variants are a major cause of drug resistance in cancer, but for most variants their effects on drug response are yet unknown. W [...]
21 July 15:10-15:30 (add to calendar)	01C		Single Cell Spatial Transcriptomics: Decoding Cellular Heterogeneity in Spatial Dimensions	ISCB-China Workshop
21 July 15:10-15:20 (add to calendar)	01A	Line Sandvad Nielsen	NetStart 2.0: Prediction of Eukaryotic Translation Initiation Sites Using a Protein Language Model	MLCSB: Machine Learning in Computational and Systems Biology	"Background: Accurate identification of translation initiation sites is essential for the proper translation of mRNA into functional proteins. In euka [...]
21 July 15:15-15:30 (add to calendar)	12	Elizabeth Fahsbender	Benchmarking in Service of Virtual Cell Models: Challenges, Opportunities, and a Path Forward	DREAM Challenges	Realizing the vision of AI-powered Virtual Cells demands robust and biologically meaningful benchmarks that ensure models are reliable, reproducible, [...]
21 July 15:20-15:40 (add to calendar)	03B	Xiangru Tang	BC-Design: A Biochemistry-Aware Framework for Highly Accurate Inverse Protein Folding	3DSIG: Structural Bioinformatics and Computational Biophysics	Inverse protein folding, which aims to design amino acid sequences for desired protein structures, is fundamental to protein engineering and therapeut [...]
21 July 15:20-15:40 (add to calendar)	03A	Aziz Khan	JASPAR-Suite: An open toolkit for accessing TF binding motifs	BOSC: Bioinformatics Open Source Conference	JASPAR database (https://jaspar.elixir.no) is a widely used open-access database of manually curated, non-redundant transcription factor (TF) binding [...]
21 July 15:20-15:40 (add to calendar)	03A	Sebastian Ayala-Ruano	VueGen: automating the generation of scientific reports	BOSC: Bioinformatics Open Source Conference	The analysis of omics data typically involves multiple bioinformatics tools and methods, each producing distinct output files. However, compiling thes [...]
21 July 15:20-15:40 (add to calendar)	03A	Bryan Cosca	The world’s biomedical knowledge in less than a gram: introducing the PGP incubator	BOSC: Bioinformatics Open Source Conference	In this talk, we describe a new project, the Personal Genome Project incubator. The PGPincubator is an effort to create a distribution of open data, [...]
21 July 15:20-15:40 (add to calendar)	01B	Charles Gadd	SurvivEHR: A Primary Care Foundation Prediction Model for Multiple Long-Term Conditions	Bioinformatics in the UK	We present SurvivEHR, a foundation model for time-to-event prediction using Electronic Health Records (EHR), based on the Generative Pre-trained Trans [...]
21 July 15:20-15:40 (add to calendar)	11BC	Adam Gudys	Accurate multiple sequence alignment at protein-universe scale with FAMSA 2	EvolCompGen: Evolution & Comparative Genomics	Multiple sequence alignment (MSA) is a crucial analysis in computational biology applied, e.g., in phylogeny reconstruction or protein function predic [...]
21 July 15:20-15:40 (add to calendar)	02N	Mohamed Reda Keddar	Pan-cancer analysis in the real-world setting uncovers immunogenomic drivers of acquired resistance post-immunotherapy	GenCompBio: General Computational Biology	Immune checkpoint blockade (ICB) has transformed cancer care, procuring long-lasting benefit to patients across various cancer types. However, >80% of [...]
21 July 15:20-15:30 (add to calendar)	01A	Uxía Veleiro	Towards a more inductive world for drug repurposing approaches	MLCSB: Machine Learning in Computational and Systems Biology	Drug–target interaction (DTI) prediction is a challenging albeit essential task in drug repurposing. Learning on graph models has drawn special attent [...]
21 July 15:20-15:40 (add to calendar)	02F	Jared Rozowsky	Power Your Kids First or INCLUDE Data Analysis on The Interoperable CAVATICA Cloud Analytics Workspace	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	The NIH-funded Gabriella Miller Kids First Data Resource Center (KF-DRC) and the INCLUDE Data Coordinating Center (INCLUDE DCC) provide harmonized dat [...]
21 July 15:20-15:40 (add to calendar)	11A	Stephen Williams	Revving up insights in single cell and spatial exploration	Tech Track	10x Genomics will present a comprehensive overview of our cutting-edge technologies: Visium for spatial transcriptomics, Chromium for single-cell anal [...]
21 July 15:20-15:30 (add to calendar)	04AB	Ning Shen	SpliceTransformer predicts tissue-specific splicing linked to human diseases	VarI: Variant Interpretation	We present SpliceTransformer (SpTransformer), a deep-learning framework that predicts tissue-specific RNA splicing alterations linked to human disease [...]
21 July 15:30-16:00 (add to calendar)	12	Anshul Kundaje	Deep learning models of regulatory DNA: A critical analysis of model design choices	DREAM Challenges	Keynote: Gene expression is tightly regulated by complexes of proteins that interpret complex sequence syntax encoded in regulatory DNA. Genetic varia [...]
21 July 15:30-16:00 (add to calendar)	01C		Bioinformatics @ China	ISCB-China Workshop
21 July 15:30-15:40 (add to calendar)	01A	Nhung Duong	Hierarchical Multi-Agent Reinforcement Learning For Optimizing CRISPR-Based Polygenic Therapeutic Design	MLCSB: Machine Learning in Computational and Systems Biology	Background. CRISPR therapies for polygenic disorders require simultaneous optimization of multiple guides and delivery constraints. Current approaches [...]
21 July 15:30-15:40 (add to calendar)	04AB	Dennis Hecker	Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci	VarI: Variant Interpretation	Coronary artery disease (CAD) is the leading cause of death worldwide. Recently, hundreds of genomic loci have been shown to increase CAD risk, howeve [...]
21 July 15:40-16:00 (add to calendar)	03B	Xinyi Zhou	DivPro: Diverse Protein Sequence Design with Direct Structure Recovery Guidance	3DSIG: Structural Bioinformatics and Computational Biophysics	Motivation: Structure-based protein design is crucial for designing proteins with novel structures and functions, which aims to generate sequences tha [...]
21 July 15:40-16:00 (add to calendar)	03A	Jim Procter	Slivka: a new ecosystem for wrapping local code as web services	BOSC: Bioinformatics Open Source Conference	Slivka is a Python/Flask/MongoDB framework that allows command line tools to be made available as web services through creation of a YAML document tha [...]
21 July 15:40-15:50 (add to calendar)	01B	David Yuan	Pathogen Analysis System (PAS): A Scalable Genomic Data Processing Framework Integrated with the European Nucleotide Archive	Bioinformatics in the UK	The Pathogen Data Network (PDN) consists of two interconnected networks: local private data hubs for public health and global public knowledge bases f [...]
21 July 15:40-16:00 (add to calendar)	11BC	Erik Wright	Community detection at unprecedented scales with ExoLabel	EvolCompGen: Evolution & Comparative Genomics	Many approaches in comparative genomics rely on clusters of orthologous genes (COGs). Methods for constructing COGs often employ community detection a [...]
21 July 15:40-16:00 (add to calendar)	02N	Komlan Atitey	Beyond Mutation Frequency: A Bayesian Framework for Identifying Functional Cancer Drivers from Single-Cell Data	GenCompBio: General Computational Biology	Cancer is driven by genetic alterations, especially gain-of-function mutations in oncogenes (OGs) and loss-of-function mutations in tumor suppressor g [...]
21 July 15:40-15:50 (add to calendar)	01A	Luyang Li	Developing a Deep Learning Model for Single-Cell RNA Splicing Analysis	MLCSB: Machine Learning in Computational and Systems Biology	Approximately 95% of human genes undergo alternative splicing (AS), a process that allows a single gene to produce multiple proteins with distinct fun [...]
21 July 15:40-16:00 (add to calendar)	02F	Julie Jurgens	The Gene Set Browser: An interoperable and AI/ML-ready tool for gene set analysis in the Common Fund Data Ecosystem (CFDE)	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	Summary: This session introduces the NIH Common Fund Data Ecosystem (CFDE) Gene Set Browser, an AI/ML-ready tool that connects diverse biomedical dat [...]
21 July 15:40-16:00 (add to calendar)	11A	Severin Dicks	The Next Generation of scverse - Tools for Scalable Single-Cell Analysis	Tech Track	Scverse is a modular, open-source ecosystem for scalable single-cell omics analysis. It provides standardized data structures through AnnData, MuData, [...]
21 July 15:40-15:50 (add to calendar)	04AB	Ritwiz Kamal	MultiPopPred: A Trans-Ethnic Disease Risk Prediction Method, and its Evaluation on Low Resource Populations	VarI: Variant Interpretation	Genome-wide association studies (GWAS) aimed at estimating the disease risk of genetic factors have long been focusing on homogeneous Caucasian popula [...]
21 July 15:50-16:00 (add to calendar)	01B	Heba Sailem	AI in Histopathology Explorer for comprehensive analysis of the evolving AI landscape in histopathology	Bioinformatics in the UK	Digital pathology and artificial intelligence (AI) hold immense transformative potential to revolutionize cancer diagnostics, treatment outcomes, and [...]
21 July 15:50-16:00 (add to calendar)	01A	Francesca Cuturello	Evolutionary constraints guide AlphaFold2 in predicting alternative conformations and inform rational mutation design	MLCSB: Machine Learning in Computational and Systems Biology	Investigating structural variability is essential for understanding protein biological functions. Although AlphaFold2 accurately predicts static struc [...]
21 July 15:50-16:00 (add to calendar)	04AB	Huijiao Yang	Rethink gender as confounder in non linear PRS for human height prediction	VarI: Variant Interpretation	Polygenic risk score (PRS) models often include gender as a fixed covariate, implicitly assuming a direct and additive effect on traits such as height [...]
21 July 16:40-16:50 (add to calendar)	03B	Dmitry Molodenskiy	AlphaPulldown2—a general pipeline for high-throughput structural modeling	3DSIG: Structural Bioinformatics and Computational Biophysics	AlphaPulldown2 streamlines protein structural modeling by automating workflows, improving code adaptability, and optimizing data management for large- [...]
21 July 16:40-17:00 (add to calendar)	03A	Munazah Andrabi	FAIRDOM-SEEK: Platform for FAIR data and research asset management	BOSC: Bioinformatics Open Source Conference	As research becomes more data-driven, collaborative, and interdisciplinary, the need for structured, accessible, and well-curated data outputs with ri [...]
21 July 16:40-17:00 (add to calendar)	01B	Mo Lotfollahi	Generative machine learning to model cellular perturbations	Bioinformatics in the UK	The field of cellular biology has long sought to understand the intricate mechanisms that govern cellular responses to various perturbations, be they [...]
21 July 16:40-16:55 (add to calendar)	12	Justin Guinney	Benchmarking Multi-Modal Large Language Models for Metastatic Breast Cancer Prognosis	DREAM Challenges	Inputs into cancer prognostic models are primarily structured data such as demographic and clinicopathological features, and lack richer and temporal [...]
21 July 16:40-17:00 (add to calendar)	11BC	Charles Bernard	EdgeHOG: Scalable and Fine-Grained Ancestral Gene Order Inference Across the Tree of Life	EvolCompGen: Evolution & Comparative Genomics	Ancestral genomes are essential for studying the diversification of life from the last universal common ancestor to modern organisms. Methods have bee [...]
21 July 16:40-17:00 (add to calendar)	02N	Nadine S. Kurz	AdaGenes: A streaming processor for high-throughput annotation and filtering of sequence variant data	GenCompBio: General Computational Biology	The amount of sequencing data resulting from whole exome or genome sequencing (WES / WGS) presents challenges for annotation, filtering, and analysis. [...]
21 July 16:40-17:10 (add to calendar)	01C		Learning Multiscale Cellular Organization and Interaction	ISCB-China Workshop
21 July 16:40-16:50 (add to calendar)	01A	Nikolaos Meimetis	Integrating Machine Learning and Systems Biology to rationally design operational conditions for in vitro / in vivo translation of microphysiological systems	MLCSB: Machine Learning in Computational and Systems Biology	Preclinical models are used extensively to study diseases and potential therapeutic treatments. Complex in vitro platforms incorporating human cellula [...]
21 July 16:40-17:00 (add to calendar)	02F	Fenglou Mao	NIH Quantum Computing Initiatives	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing
21 July 16:40-17:20 (add to calendar)	04AB	Andrew Lawson	Somatic mutations in normal tissues	VarI: Variant Interpretation	As we age, all cells in our bodies continuously acquire somatic mutations. Despite appearing histologically normal, many tissues become progressively [...]
21 July 16:50-17:00 (add to calendar)	03B	Michel van Kempen	Extending 3Di: Increasing Protein Structure Search Sensitivity with a Complementary Alphabet	3DSIG: Structural Bioinformatics and Computational Biophysics	Fast protein structure search methods, such as Foldseek, are essential to make use of the vast amount of structural information generated by structure [...]
21 July 16:50-17:00 (add to calendar)	01A	Roman Joeres	Data Splitting Against Information Leakage with DataSAIL	MLCSB: Machine Learning in Computational and Systems Biology	Information leakage (IL) is an increasingly important topic in machine learning (ML) research, especially in biomedical applications. When IL happens [...]
21 July 16:55-17:30 (add to calendar)	12		Crowdsourcing Experiment	DREAM Challenges	We will collectively conduct a small scale community experiment to simulate a large scale crowdsourcing initiative to benchmark foundation models. [...]
21 July 17:00-17:10 (add to calendar)	03B	Justas Dapkunas	PPI3D clusters: non-redundant datasets of protein-protein, protein-peptide and protein-nucleic acid complexes, interaction interfaces and binding sites	3DSIG: Structural Bioinformatics and Computational Biophysics	To accomplish their functions in living organisms, proteins usually interact with various biological macromolecules, including other proteins and nucl [...]
21 July 17:00-17:20 (add to calendar)	03A	Jimmy Payyappilly	Walkthrough of GA4GH standards and interoperability it provides for genomic data implementations	BOSC: Bioinformatics Open Source Conference	The sharing of genomic and health-related data for biomedical research is of key importance in ensuring continued progress in our understanding of hum [...]
21 July 17:00-17:20 (add to calendar)	03A	Laura Godfrey	LiMeTrack: A lightweight biosample management platform for the multicenter SATURN3 consortium	BOSC: Bioinformatics Open Source Conference	Biomedical research projects involving large patient cohorts are increasingly complex, both in terms of data modalities and number of samples. Hence, [...]
21 July 17:00-17:20 (add to calendar)	03A	Rachel Seongeun Kim	BFVD – A release of 351k viral protein structure predictions	BOSC: Bioinformatics Open Source Conference	While the AlphaFold Protein Structure Database (AFDB) is the largest resource of accurately predicted structures – covering 214 million UniProt entrie [...]
21 July 17:00-17:10 (add to calendar)	01B	Carla Greco	Building the world’s largest, ethically-sourced database of biological information to pioneer a new class of foundational AI models	Bioinformatics in the UK	Foundational AI models are revolutionizing many fields, but their effectiveness hinges on the availability of high-quality, diverse data. Without a ro [...]
21 July 17:00-17:20 (add to calendar)	11BC	Sophia Chirrane	JIGSAW: Accurate inference of exact copy numbers from targeted single-cell DNA sequencing	EvolCompGen: Evolution & Comparative Genomics	Tumorigenesis is driven by the interplay between somatic single-nucleotide variants (SNVs) and larger structural alterations, like copy number alterat [...]
21 July 17:00-17:20 (add to calendar)	02N	Serghei Mangul	Comprehensive framework for assessing discrepancies in genomic content and species-level annotations across microbial reference genomes	GenCompBio: General Computational Biology	Metagenomics research provides insights into the composition, diversity, and functions of microbial communities in various environments. To identify b [...]
21 July 17:00-18:00 (add to calendar)	01A	Maria Brbic	Generative AI for Unlocking the Complexity of Cells	MLCSB: Machine Learning in Computational and Systems Biology	We are witnessing an AI revolution. At the heart of this revolution are generative AI models that, powered by advanced architectures and large dataset [...]
21 July 17:00-17:20 (add to calendar)	02F	Chi Zhang	Advancing quantum algorithms for elementary mode and metabolic flux analysis	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	Metabolic networks play a central role in cellular function, supporting energy production, biosynthesis, and adaptation to environmental conditions. E [...]
21 July 17:10-17:30 (add to calendar)	03B	Su Datt Lam	From GWAS to Protein Structures: Illuminating Stress Resistance in Plants	3DSIG: Structural Bioinformatics and Computational Biophysics	Plants face significant environmental stress such as pathogens, salinity, drought, and extreme temperatures. To survive, they evolve diverse adaptive [...]
21 July 17:10-17:20 (add to calendar)	01B	Arijit Patra	Multimodal generative machine learning for non-clinical safety evaluations in drug discovery and development	Bioinformatics in the UK	In the evolving landscape of pharmaceutical drug development and a constant reimagination of the Ideas to Patient journey, the integration of multimod [...]
21 July 17:10-17:30 (add to calendar)	01C	James Zou	Language-guided biology	ISCB-China Workshop	Large language models (LLMs), such as ChatGPT, have read millions of papers and contains tremendous biomedical knowledge. In language-guided biology, [...]
21 July 17:20-17:40 (add to calendar)	03A	Monica Munoz-Torres	AI-readiness for biomedical data: Bridge2AI recommendations	BOSC: Bioinformatics Open Source Conference	The convergence of biomedical research and artificial intelligence (AI) promises unprecedented insights into complex biological systems. However, real [...]
21 July 17:20-17:30 (add to calendar)	01B	Steven M. Hill	CUPiD: a machine learning approach for determining tissue-of-origin in cancers of unknown primary from cell-free DNA methylation profiles	Bioinformatics in the UK	Patients with cancer of unknown primary (CUP) present with metastases, but without an identifiable primary tumour and typically have poor outcomes. De [...]
21 July 17:20-17:40 (add to calendar)	11BC	Ricardo C. Rodriguez de la Vega	EASYstrata: a fully integrated workflow to infer evolutionary strata along sex chromosomes and other supergenes	EvolCompGen: Evolution & Comparative Genomics	New reference-level genomes are becoming increasingly available across the tree of life, opening new avenues for addressing exciting evolutionary ques [...]
21 July 17:20-17:40 (add to calendar)	02N	Sumit Walia	Building Ultralarge Pangenomes Using Scalable and Compressive Techniques	GenCompBio: General Computational Biology	Pangenomics studies intra-species genetic diversity by analyzing collections of genomes from the same species. As pangenomics scales to millions of se [...]
21 July 17:20-17:40 (add to calendar)	02F	Vischi Michele	Efficient quantum algorithm to simulate open systems through a single environmental qubit	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing	Simulating the dynamics of open quantum systems allows to understand real-world quantum phenomena which is a crucial task in a variety of fields. Rece [...]
21 July 17:20-17:40 (add to calendar)	04AB	Michal Linial	Revisiting Cancer Predisposition: Identifying Altered Genes with Protective and Recessive Effects	VarI: Variant Interpretation	essential for both preventive and personalized medicine. Genetic studies of cancer predisposition typically identify significant genomic regions throu [...]
21 July 17:30-17:40 (add to calendar)	03B	Sevastianos Korsak	Chromatin as a Coevolutionary Graph: Modeling the Interplay of Replication with Chromatin Dynamics	3DSIG: Structural Bioinformatics and Computational Biophysics	Modeling DNA replication poses significant challenges due to the intricate interplay of biophysical processes and the need for precise parameter optim [...]
21 July 17:30-17:35 (add to calendar)	01B	Charlie Harrison	Introduction to AIBIO UK	Bioinformatics in the UK	AIBIO-UK is a UKRI BBSRC-funded network to support and enhance engagement between the Biosciences and AI communities in the UK. The network supports [...]
21 July 17:30-18:00 (add to calendar)	12		Evaluating and Benchmarking Foundation Models	DREAM Challenges	Speakers will give their opinions and about best practices to evaluate foundation models in biomedicine, and engage in conversation with attendees. [...]
21 July 17:30-18:00 (add to calendar)	01C		AI and Bioinformatics: The Next Era	ISCB-China Workshop
21 July 17:35-18:00 (add to calendar)	01B		AI: Careers and trajectories	Bioinformatics in the UK	TBC [...]
21 July 17:40-18:00 (add to calendar)	03B	Clément Bernard	RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction	3DSIG: Structural Bioinformatics and Computational Biophysics	Predicting the 3D structure of RNA is an ongoing challenge that has yet to be completely addressed despite continuous advancements. RNA 3D structures [...]
21 July 17:40-17:50 (add to calendar)	03A	Susheel Varma	Bridging the gap: advancing aging & dementia research through the open-access AD Knowledge Portal	BOSC: Bioinformatics Open Source Conference	The AD Knowledge Portal (adknowledgeportal.org) is an NIA-funded resource developed by Sage Bionetworks to facilitate Alzheimer's Disease research thr [...]
21 July 17:40-18:00 (add to calendar)	11BC	Suvojit Hazra	The Phylogenetic Dynamic Regulatory Module Networks (P-DRMN) study infers Cis-regulatory features responsible for evolution of mammalian gene regulatory programs in aortic endothelium	EvolCompGen: Evolution & Comparative Genomics	Cis-regulatory elements (CREs), such as promoters and enhancers, interact with transcription factors (TFs) to drive gene regulatory programs and contr [...]
21 July 17:40-18:00 (add to calendar)	02N	Melissa Sanabria	Information Content as a metric to evaluate and compare DNA Language Models	GenCompBio: General Computational Biology	Large language models have transformed the field of natural language processing by enabling the generation of coherent and meaningful text. This succe [...]
21 July 17:40-18:00 (add to calendar)	02F	Yong Chen	Quantum Approximate Optimization for K-Area Clustering of Biological Data	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing
21 July 17:40-17:50 (add to calendar)	04AB	Antoine Favier	COBT: A gene-based rare variant burden test for case-only study designs using aggregated genotypes from public reference cohorts	VarI: Variant Interpretation	More than 4000 rare genetic diseases have been reported, affecting 1 in 16 people. Yet, around 50% of patients remain undiagnosed after genetic testin [...]
21 July 17:50-18:00 (add to calendar)	03A	Susheel Varma	The ELITE Portal: A FAIR Data Resource For Healthy Aging Over The Life Span	BOSC: Bioinformatics Open Source Conference	Exceptional longevity (EL) is a rare phenotype characterized by an extended health span and sustained physiological function. Various domain-specific [...]
21 July 17:50-18:00 (add to calendar)	04AB		Concluding remarks and prizes	VarI: Variant Interpretation
21 July 18:00-18:00 (add to calendar)	02F		Closing Remarks	NIH Track on GenAI, Cyberinfrastructure, Digital Twins, and Quantum Computing
22 July 08:40-09:00 (add to calendar)	01A	-	Morning Welcome and Keynote Introduction	Distinguished Keynotes
22 July 09:00-10:00 (add to calendar)	01A	James Zou	Computational biology in the age of AI agents	Distinguished Keynotes	AI agents—large language models equipped with tools and reasoning capabilities-are emerging as powerful research enablers. This talk will explore how [...]
22 July 11:20-12:00 (add to calendar)	03B	Diego Ulises Ferreiro	A (bio)computational perspective on protein folding, function and evolution	3DSIG: Structural Bioinformatics and Computational Biophysics	Natural protein molecules are amazing objects that somehow compute their structure, dynamics, and activities given a sequence of amino acids and an en [...]
22 July 11:20-12:20 (add to calendar)	03A	Chris Mungall	Open Knowledge Bases in the Age of Generative AI	BOKR: Bio-Ontologies and Knowledge Representation	The scientific and clinical community relies on the active development of a wide range of inter-linked knowledge bases, in order to plan experiments, [...]
22 July 11:20-12:20 (add to calendar)	03A	Chris Mungall	Open Knowledge Bases in the Age of Generative AI	BOSC: Bioinformatics Open Source Conference	The scientific and clinical community relies on the active development of a wide range of inter-linked knowledge bases, in order to plan experiments, [...]
22 July 11:20-12:00 (add to calendar)	04AB	Julio Saez-Rodriguez	Knowledge-based machine learning to study cellular regulation from spatial multi-omics data	CSI: Computational Systems Immunology	Multi-omics technologies, specially with single-cell and spatial resolution, provide unique opportunities to the key study intra- and inter-cellular p [...]
22 July 11:20-12:00 (add to calendar)	02F	Warwick Dunn	The elephant in the (metabolomics) room: computational approaches for small molecule structural annotation from single biological study to data repositories	CompMS: Computational Mass Spectrometry	Multiple omics research strategies (metabolomics, lipidomics, exposomics) focus on the reporting of small molecules in biological systems in relation [...]
22 July 11:20-11:30 (add to calendar)	12		Introduction	EvolCompGen: Evolution & Comparative Genomics	Introduction to the joint session Function and EvolCompGen [...]
22 July 11:20-11:30 (add to calendar)	12		Introduction	Function: Gene and Protein Function Annotation	Introduction to the joint session Function and EvolCompGen [...]
22 July 11:20-12:20 (add to calendar)	01A	Maria Chikina	Toward Mechanistic Genomics: Advances in Sequence-to-Function Modeling	MLCSB: Machine Learning in Computational and Systems Biology	Recent advances have firmly established sequence-to-function models as essential tools in modern genomics, enabling unprecedented insights into how ge [...]
22 July 11:20-12:00 (add to calendar)	01B	Laura Cantini	Multi-modal learning for single-cell data integration	NetBio: Network Biology	Single-cell RNA sequencing (scRNAseq) is revolutionizing biology and medicine. The possibility to assess cellular heterogeneity at a previously inacce [...]
22 July 11:20-11:30 (add to calendar)	01C		Opening Talk	SysMod: Computational Modeling of Biological Systems	The community of special interest (COSI) in systems modeling (SysMod) organizes annual one-day gatherings. In 2025 the meeting comprises three session [...]
22 July 11:20-11:40 (add to calendar)	11A	Adam Talbot	Scale with Seqera: Accelerate, Expand, and Collaborate	Tech Track	Turning a promising research project into a robust, real-world solution requires tools that support both early experimentation and enterprise-scale de [...]
22 July 11:20-11:30 (add to calendar)	02N		Welcome and opening remarks	TransMed: Translational Medicine Informatics & Applications
22 July 11:30-12:10 (add to calendar)	12	Marc Robinson-Rechavi	Evolution of function in light of gene expression	EvolCompGen: Evolution & Comparative Genomics	One of the fundamental questions of genome evolution is how gene function changes or is constrained, whether between species (orthologs) or inside gen [...]
22 July 11:30-12:10 (add to calendar)	12	Marc Robinson-Rechavi	Evolution of function in light of gene expression	Function: Gene and Protein Function Annotation	One of the fundamental questions of genome evolution is how gene function changes or is constrained, whether between species (orthologs) or inside gen [...]
22 July 11:30-12:10 (add to calendar)	01C	Ronan Fleming	Variational kinetics: a variational formulation of reaction kinetics	SysMod: Computational Modeling of Biological Systems	Established genome-scale modelling methods primarily predict reaction fluxes while established high-throughput experimental technologies primarily mea [...]
22 July 11:30-12:10 (add to calendar)	02N	Melanie Schirmer	Gene-centric metagenomic analysis reveals functional insights into disease	TransMed: Translational Medicine Informatics & Applications	The human microbiome encodes millions of microbial genes that play a critical role for our health. However, identifying disease-associated microbial g [...]
22 July 11:40-12:00 (add to calendar)	11A	Viktor Rudko	SimpleVM - Effortless Cloud Computing for Research	Tech Track	SimpleVM empowers life science researchers to harness cloud resources, regardless of their expertise in cloud computing. As a multi-cloud application, [...]
22 July 12:00-12:20 (add to calendar)	03B	David Moi	Structural Phylogenetics: toward an evolutionary model capturing both sequence and structure	3DSIG: Structural Bioinformatics and Computational Biophysics	Inferring deep phylogenetic relationships between proteins requires methods that can capture the iterative optimisation of the final folded protein ob [...]
22 July 12:00-12:20 (add to calendar)	04AB	Robert F. Murphy	Flexible and robust cell type annotation for highly multiplexed tissue images	CSI: Computational Systems Immunology	Identifying cell types in highly multiplexed images is essential for understanding tissue spatial organization. Current cell type annotation methods o [...]
22 July 12:00-12:20 (add to calendar)	02F	Madina Bekbergenova	MetaboT: AI-based agent for natural language-based interaction with metabolomics knowledge graphs	CompMS: Computational Mass Spectrometry	Long abstract is submitted in pdf [...]
22 July 12:00-12:20 (add to calendar)	01B	Mayra Luisa Ruiz Tejada Segura	Nichesphere: A method to identify disease specific physical cell-cell interactions and underlying cellular communication networks	NetBio: Network Biology	Understanding disease specific cellular crosstalk is crucial for therapeutic targeting but challenging as signaling pathways dependent on direct physi [...]
22 July 12:00-12:20 (add to calendar)	11A	Mitchell Shiell	Overture Prelude: A toolkit for small teams with big data problems	Tech Track	Overture is used to build platforms that enable researchers to organize and share their data quickly, flexibly and at multiple scales. While Overture [...]
22 July 12:10-12:20 (add to calendar)	12	Erik Wright	Convergent evolution to similar proteins confounds structure search	EvolCompGen: Evolution & Comparative Genomics	Advances in protein structure prediction and structural search tools (e.g., FoldSeek and PLMSearch) have enabled large-scale comparison of protein str [...]
22 July 12:10-12:20 (add to calendar)	12	Erik Wright	Convergent evolution to similar proteins confounds structure search	Function: Gene and Protein Function Annotation	Advances in protein structure prediction and structural search tools (e.g., FoldSeek and PLMSearch) have enabled large-scale comparison of protein str [...]
22 July 12:10-12:30 (add to calendar)	01C	Shauna O'Donovan	A dynamic multi-tissue metabolic reconstruction reveals interindividual variation in postprandial metabolic fluxes	SysMod: Computational Modeling of Biological Systems	Genome-scale metabolic models (GEMs) are large network-based metabolic reconstructions that can predict the flux of numerous metabolites making them v [...]
22 July 12:10-12:30 (add to calendar)	02N	Mirko Treccani	How (poly)phenols can shape a healthier life? A nutri-omics investigation on their cardiometabolic health effects	TransMed: Translational Medicine Informatics & Applications	(Poly)phenols (PPs) are a group of bioactive compounds found in plant-based food, widely consumed within diet. Several studies have reported the benef [...]
22 July 12:20-12:40 (add to calendar)	03B	Joel Roca Martinez	The structural and functional plasticity of the GNAT fold: A case of convergent evolution	3DSIG: Structural Bioinformatics and Computational Biophysics	Spermine/spermidine acetyltransferases (SSATs) are members of the highly diverse Gcn5-related N-acetyltransferase (GNAT) superfamily, which ranks amon [...]
22 July 12:20-12:40 (add to calendar)	03A	Favour James	textToKnowledgeGraph: Generation of Molecular Interaction Knowledge Graphs Using Large Language Models for Exploration in Cytoscape	BOKR: Bio-Ontologies and Knowledge Representation	Knowledge graphs (KGs) are powerful tools for structuring and analyzing biological information due to their ability to represent data and improve quer [...]
22 July 12:20-12:40 (add to calendar)	03A	Favour James	textToKnowledgeGraph: Generation of Molecular Interaction Knowledge Graphs Using Large Language Models for Exploration in Cytoscape	BOSC: Bioinformatics Open Source Conference	Knowledge graphs (KGs) are powerful tools for structuring and analyzing biological information due to their ability to represent data and improve quer [...]
22 July 12:20-12:40 (add to calendar)	04AB	Haoyu Wang	Dual-Graph Attention Network for Protein Imputation from Spatial Transcriptomics	CSI: Computational Systems Immunology	Cell function in multicellular systems is shaped by its spatial context, making the study of cellular interactions within tissues essential for unders [...]
22 July 12:20-12:40 (add to calendar)	02F	Alejandro Mendoza Cantu	Reference data-driven analysis for joint metabolome–microbiome readout from untargeted mass spectrometry data	CompMS: Computational Mass Spectrometry	Untargeted tandem mass spectrometry (MS/MS) metabolomics enables broad chemical profiling of complex biological samples but is limited by low annotati [...]
22 July 12:20-12:30 (add to calendar)	12	Maureen Stolzer	Evolution of the Metazoan Protein Domain Toolkit Revealed by a Birth-Death-Gain Model	EvolCompGen: Evolution & Comparative Genomics	Domains, sequence fragments that encode protein modules with a distinct structure and function, are the basic building blocks of proteins. The set of [...]
22 July 12:20-12:30 (add to calendar)	12	Maureen Stolzer	Evolution of the Metazoan Protein Domain Toolkit Revealed by a Birth-Death-Gain Model	Function: Gene and Protein Function Annotation	Domains, sequence fragments that encode protein modules with a distinct structure and function, are the basic building blocks of proteins. The set of [...]
22 July 12:20-12:40 (add to calendar)	01A	Judith Bernett	Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65	MLCSB: Machine Learning in Computational and Systems Biology	As most proteins interact with other proteins to perform their respective functions, methods to computationally predict these interactions have been d [...]
22 July 12:20-12:40 (add to calendar)	01B	Saniya Khullar	NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation	NetBio: Network Biology	Background: Transcription factor (TF) coordination plays a key role in gene regulation via direct and/or indirect protein–protein interactions (PPIs) [...]
22 July 12:20-13:00 (add to calendar)	11A	Filippo Utro	AI and Quantum in Healthcare and Life Sciences	Tech Track	The advent of foundation models (FM) and quantum computing (QC) has ushered in a new paradigm for tackling complex problems, igniting significant inte [...]
22 July 12:30-12:40 (add to calendar)	12	Samuel Davis	Deep Phylogenetic Reconstruction Reveals Key Functional Drivers in the Evolution of B1/B2 Metallo-β-Lactamases	EvolCompGen: Evolution & Comparative Genomics	Metallo-β-lactamases (MBLs) comprise a diverse family of antibiotic-degrading enzymes. Despite their growing implication in drug-resistant pathogens, [...]
22 July 12:30-12:40 (add to calendar)	12	Samuel Davis	Deep Phylogenetic Reconstruction Reveals Key Functional Drivers in the Evolution of B1/B2 Metallo-β-Lactamases	Function: Gene and Protein Function Annotation	Metallo-β-lactamases (MBLs) comprise a diverse family of antibiotic-degrading enzymes. Despite their growing implication in drug-resistant pathogens, [...]
22 July 12:30-12:50 (add to calendar)	01C	Garhima Arora	Decoding organ-specific breast cancer metastasis through single-cell metabolic modeling	SysMod: Computational Modeling of Biological Systems	Breast organotropism, the preferential metastasis of breast cancer cells to specific organs, remains a critical challenge but clinically significant p [...]
22 July 12:30-12:40 (add to calendar)	02N	Mehdi Layeghifard	Genomic Scars of Survival: Translating Therapy-Induced Mutagenesis into Clinical Insights in Childhood Cancer	TransMed: Translational Medicine Informatics & Applications	Children with cancer endure numerous short- and long-term side effects of treatment, but the extent of DNA damage associated with chemotherapy exposur [...]
22 July 12:40-13:00 (add to calendar)	03B	Wan-Chun Su	Virus targeting as a dominant driver of interfacial evolution in the structurally resolved human-virus protein-protein interaction network	3DSIG: Structural Bioinformatics and Computational Biophysics	The competitive nature of host-virus protein-protein interactions drives an ongoing evolutionary arms race between hosts and viruses. The surface regi [...]
22 July 12:40-13:00 (add to calendar)	03A	Bharath Dandala	BMFM-RNA: An Open Framework for Building and Evaluating Transcriptomic Foundation Models built on Biomed-Multi-Omic	BOKR: Bio-Ontologies and Knowledge Representation	High-throughput sequencing has revolutionized transcriptomic studies, and the synthesis of these diverse datasets holds significant potential for a de [...]
22 July 12:40-13:00 (add to calendar)	03A	Gavin Farrell	DOME Registry - Supporting ML transparency and reproducibility in the life sciences	BOKR: Bio-Ontologies and Knowledge Representation	The adoption of machine learning (ML) methods in the life sciences has been transformative, solving landmark challenges such as accurate protein struc [...]
22 July 12:40-13:00 (add to calendar)	03A	Raúl Fernández-Díaz	AutoPeptideML 2: An open source library for democratizing machine learning for peptide bioactivity prediction	BOKR: Bio-Ontologies and Knowledge Representation	Peptides are a rapidly growing drug modality with diverse bioactivities and accessible synthesis, particularly for canonical peptides composed of the [...]
22 July 12:40-13:00 (add to calendar)	03A	Bharath Dandala	BMFM-RNA: An Open Framework for Building and Evaluating Transcriptomic Foundation Models built on Biomed-Multi-Omic	BOSC: Bioinformatics Open Source Conference	High-throughput sequencing has revolutionized transcriptomic studies, and the synthesis of these diverse datasets holds significant potential for a de [...]
22 July 12:40-13:00 (add to calendar)	03A	Gavin Farrell	DOME Registry - Supporting ML transparency and reproducibility in the life sciences	BOSC: Bioinformatics Open Source Conference	The adoption of machine learning (ML) methods in the life sciences has been transformative, solving landmark challenges such as accurate protein struc [...]
22 July 12:40-13:00 (add to calendar)	03A	Raúl Fernández-Díaz	AutoPeptideML 2: An open source library for democratizing machine learning for peptide bioactivity prediction	BOSC: Bioinformatics Open Source Conference	Peptides are a rapidly growing drug modality with diverse bioactivities and accessible synthesis, particularly for canonical peptides composed of the [...]
22 July 12:40-13:00 (add to calendar)	04AB	Veronika Kedlian	Single-cell and spatial atlas of the Human Ageing Thymus	CSI: Computational Systems Immunology	The thymus is a primary immune organ responsible for the production of naive T cells which experiences age-related changes, also termed involution ver [...]
22 July 12:40-13:00 (add to calendar)	02F	Diana Karaki	Combined MS and MS/MS deconvolution of SWATH DIA data with the DIA-NMF software for comprehensive annotation in metabolomics	CompMS: Computational Mass Spectrometry	Data-independent acquisition (DIA), particularly Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS), is gaining momentum in unta [...]
22 July 12:40-13:00 (add to calendar)	02F	Nils Hoffmann	Towards mzTab-M 2.1 - Evolving the HUPO-PSI standard format for reporting of small molecule mass spectrometry results	CompMS: Computational Mass Spectrometry	Mass spectrometry (MS) is central to modern large-scale metabolomics, but a lack of data format standardization for intermediate and final MS data ana [...]
22 July 12:40-12:50 (add to calendar)	12	Paul D. Thomas	A compendium of human gene functions derived from evolutionary modeling	EvolCompGen: Evolution & Comparative Genomics	A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resour [...]
22 July 12:40-12:50 (add to calendar)	12	Paul D. Thomas	A compendium of human gene functions derived from evolutionary modeling	Function: Gene and Protein Function Annotation	A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resour [...]
22 July 12:40-13:00 (add to calendar)	01A	Jie Liu	Accurate PROTAC targeted degradation prediction with DegradeMaster	MLCSB: Machine Learning in Computational and Systems Biology	Motivation: Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that can degrade ‘undruggable’ protein of interest (POI) by recr [...]
22 July 12:40-13:00 (add to calendar)	01B	Giulia Cesaro	Cell-specific Graph Operation Strategy on Signaling Intracellular Pathways	NetBio: Network Biology	Recent advances in single-cell RNA sequencing have enabled a detailed exploration of cell-cell communication. Several computational tools infer extrac [...]
22 July 12:40-12:50 (add to calendar)	02N	Lena Möbus	MOSAIC-AD: Multilayered Patient Similarity Analysis Integrating Omics and Clinical Data for Patient Stratification in Atopic Dermatitis	TransMed: Translational Medicine Informatics & Applications	Atopic dermatitis (AD) presents with high inter-individual variability in both disease progression and treatment response. Understanding how patients [...]
22 July 12:50-13:00 (add to calendar)	12	Ana Rojas	pLM in functional annotation: relationship between sequence conservation and embedding similarity	EvolCompGen: Evolution & Comparative Genomics	Functional annotation of protein sequences remains a bottleneck for understanding the biology of both model and non model organisms, as conventional h [...]
22 July 12:50-01:00 (add to calendar)	12	Ana Rojas	pLM in functional annotation: relationship between sequence conservation and embedding similarity	Function: Gene and Protein Function Annotation	Functional annotation of protein sequences remains a bottleneck for understanding the biology of both model and non model organisms, as conventional h [...]
22 July 12:50-12:55 (add to calendar)	01C		Enzyme activation network facilitates regulatory crosstalk between metabolic pathways	SysMod: Computational Modeling of Biological Systems	The metabolic network, the largest inter connected system in the cell, is constantly regulated by a range of regulatory interactions. To characterize [...]
22 July 12:50-13:00 (add to calendar)	02N	Nicola Calonaci	Gene mutant dosage determine prognosis and metastatic tropism in 60,000 clinical cancer samples	TransMed: Translational Medicine Informatics & Applications	The intricate interplay between somatic mutations and copy number alterations critically influences tumour evolution and clinical outcomes. Yet, conve [...]
22 July 12:55-13:00 (add to calendar)	01C	Bingxin Lu	Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability	SysMod: Computational Modeling of Biological Systems	Chromosomal instability (CIN) is pervasive in human tumours and often leads to structural or numerical chromosomal aberrations. Somatic structural var [...]
22 July 14:00-14:20 (add to calendar)	03B	Nicola Bordin	Novel structural arrangements from a billion-scale protein universe	3DSIG: Structural Bioinformatics and Computational Biophysics	Recent advances in protein structure prediction by AlphaFold2 and ESMFold have massively expanded the known protein structural landscape. The AlphaFol [...]
22 July 14:00-14:20 (add to calendar)	03A	J. Harry Caufield	BioPortal: a rejuvenated resource for biomedical ontologies	BOKR: Bio-Ontologies and Knowledge Representation	BioPortal is an open repository of biomedical ontologies that supports data organization, curation, and integration across various domains. Serving as [...]
22 July 14:00-14:20 (add to calendar)	03A	J. Harry Caufield	BioPortal: a rejuvenated resource for biomedical ontologies	BOSC: Bioinformatics Open Source Conference	BioPortal is an open repository of biomedical ontologies that supports data organization, curation, and integration across various domains. Serving as [...]
22 July 14:00-14:40 (add to calendar)	04AB	Harinder Singh	Expanding the DNA Motif Lexicon of the Transcriptional Regulatory Code	CSI: Computational Systems Immunology	Transcriptional regulatory sequences in metazoans contain intricate combinations of transcription factor (TF) motifs. Stereospecific arrangements of s [...]
22 July 14:00-14:20 (add to calendar)	02F	Janne Heirman	Enhanced spectrum clustering for interpretable molecular networking	CompMS: Computational Mass Spectrometry	Small molecule tandem mass spectrometry (MS/MS) produces vast datasets, making interpretation challenging. Molecular networking aids analysis by linki [...]
22 July 14:00-14:20 (add to calendar)	11BC	Sama Goliaei	Disentangling SARS-CoV-2 Lineage Importations and the Role of NPIs Using Bayesian Phylogeography of 1.8 Million Genomes	EvolCompGen: Evolution & Comparative Genomics	Nonpharmaceutical interventions (NPIs) were key to limiting SARS-CoV-2 transmission before vaccines, though their effectiveness—especially regarding m [...]
22 July 14:00-14:20 (add to calendar)	12	Huiying Yan	GOAnnotator: Accurate protein function annotation using automatically retrieved literature	Function: Gene and Protein Function Annotation	Automated protein function prediction/annotation (AFP) is vital for understanding biological processes and advancing biomedical research. Existing tex [...]
22 July 14:00-14:20 (add to calendar)	01A	Seungheun Baek	GPO-VAE: Modeling Explainable Gene Perturbation Responses utilizing GRN-Aligned Parameter Optimization	MLCSB: Machine Learning in Computational and Systems Biology	Predicting cellular responses to genetic perturbations is essential for understanding biological systems and developing targeted therapeutic strategie [...]
22 July 14:00-14:20 (add to calendar)	01B	Sindhura Kommu	Prediction of Gene Regulatory Connections with Joint Single-Cell Foundation Models and Graph-Based Learning	NetBio: Network Biology	Motivation: Single-cell RNA sequencing (scRNA-seq) data offers unprecedented opportunities to infer gene regulatory networks (GRNs) at a fine-grained [...]
22 July 14:00-14:40 (add to calendar)	01C	Jasmin Fisher	Virtual Tumours for Predictive Precision Oncology	SysMod: Computational Modeling of Biological Systems	Cancer is a complex systemic disease driven by genetic and epigenetic aberrations that impact a multitude of signalling pathways operating in differen [...]
22 July 14:00-14:20 (add to calendar)	11A	Dorota Latek	GPCRVS - AI-driven decision support system for GPCR virtual screening	Tech Track	GPCRVS represents an efficient, simple, easily accessible, and open-source web service that, as a decision support system, aims to facilitate the prec [...]
22 July 14:00-14:20 (add to calendar)	02N	Serdar Bozdag	Top-DTI: Integrating Topological Deep Learning and Large Language Models for Drug Target Interaction Prediction	TransMed: Translational Medicine Informatics & Applications	Motivation: The accurate prediction of drug–target interactions (DTI) is a crucial step in drug discovery, providing a foundation for identifying nove [...]
22 July 14:20-14:40 (add to calendar)	03B	Hanne Zillmer	Towards a comprehensive view of the pocketome universe – biological implications and algorithmic challenges	3DSIG: Structural Bioinformatics and Computational Biophysics	With the availability of reliably predicted 3D-structures for essentially all known proteins, characterizing the entirety of protein - small-molecule [...]
22 July 14:20-14:40 (add to calendar)	03A	Michael Bouzinier	Formal Validation of Variant Classification Rules Using Domain-Specific Language and Meta-Predicates	BOKR: Bio-Ontologies and Knowledge Representation	This talk aims to initiate a community discussion on strategies for validating the selection and curation of genetic variants for clinical and researc [...]
22 July 14:20-14:40 (add to calendar)	03A	Michael Bouzinier	Formal Validation of Variant Classification Rules Using Domain-Specific Language and Meta-Predicates	BOSC: Bioinformatics Open Source Conference	This talk aims to initiate a community discussion on strategies for validating the selection and curation of genetic variants for clinical and researc [...]
22 July 14:20-14:40 (add to calendar)	02F	Juan Sebastian Piedrahita Giraldo	Deep Learning for Small Molecule Analog Discovery From Untargeted Mass Spectrometry	CompMS: Computational Mass Spectrometry	Tandem mass spectrometry (MS/MS) is a key tool for analyzing the small molecule composition of biological samples. Untargeted metabolomics data analys [...]
22 July 14:20-14:40 (add to calendar)	11BC	Nicole A. Rogowski	SARS-CoV-2 Intra-Host Evolution in Immuno-Compromised Individuals: A Fractal Perspective on Genome Geometry	EvolCompGen: Evolution & Comparative Genomics	Studies have associated the punctuated evolution of SARS-CoV-2 variants with prolonged infections and subsequent transmission. We describe the genetic [...]
22 July 14:20-14:40 (add to calendar)	12	Jun Kim	Semi-Supervised Data-Integrated Feature Importance Enhances Performance and Interpretability of Biological Classification Tasks	Function: Gene and Protein Function Annotation	Accurate model performance on training data does not ensure alignment between the model’s feature weighting patterns and human knowledge, which can li [...]
22 July 14:20-14:40 (add to calendar)	01A	Yanshuo Chen	Fast and scalable Wasserstein-1 neural optimal transport solver for single-cell perturbation prediction	MLCSB: Machine Learning in Computational and Systems Biology	Predicting single-cell perturbation responses requires mapping between two unpaired single-cell data distributions. Optimal transport (OT) theory prov [...]
22 July 14:20-14:40 (add to calendar)	01B	Ibrahim Alsaggaf	Enhanced Gaussian noise augmentation-based contrastive learning for predicting the longevity effects of genes using protein-protein interaction networks	NetBio: Network Biology	Protein-protein interaction (PPI) networks are a type of informative feature source that has already been widely used in Bioinformatics research. Howe [...]
22 July 14:20-14:40 (add to calendar)	11A	Supratim Das	Self-supervised generative AI enables conversion of two non-overlapping cohorts	Tech Track	Prognostic models in healthcare often rely on big data, which is typically distributed across multiple medical cohorts. Even if collected for similar [...]
22 July 14:20-14:30 (add to calendar)	02N	Sophia Krix	Unraveling Early Changes in Alzheimer's Disease: Causal Relationships Among Sleep Behavior, Immune Dynamics, and Cognitive Performance Through Multimodal Data Fusion	TransMed: Translational Medicine Informatics & Applications	In the early stages of Alzheimer’s Disease (AD), significant changes in sleep behavior and immune system dynamics occur prior to the onset of patholog [...]
22 July 14:30-14:40 (add to calendar)	02N	Barry Ryan	Combining Clinical Embeddings with Multi-Omic Features for Improved Interpretability in Parkinson’s Disease Patient Classification	TransMed: Translational Medicine Informatics & Applications	This study demonstrates the integration of Large Language Model (LLM)-derived clinical text embeddings from the Movement Disorder Society Unified Park [...]
22 July 14:40-14:50 (add to calendar)	03B	Miguel Fernandez-Martin	Towards a Biophysical Description of the Protein Universe	3DSIG: Structural Bioinformatics and Computational Biophysics	Understanding how protein families evolve and function remains a central question in molecular biophysics. By grouping evolutionarily related proteins [...]
22 July 14:40-15:00 (add to calendar)	03A	Sebastian Lobentanzer	BioChatter: An open-source framework integrating knowledge graphs and large language models for Accessible Biomedical AI	BOKR: Bio-Ontologies and Knowledge Representation	The integration of large language models (LLMs) with structured biomedical knowledge remains a key challenge for building robust, trustworthy, and rep [...]
22 July 14:40-15:00 (add to calendar)	03A	Sebastian Lobentanzer	BioChatter: An open-source framework integrating knowledge graphs and large language models for Accessible Biomedical AI	BOSC: Bioinformatics Open Source Conference	The integration of large language models (LLMs) with structured biomedical knowledge remains a key challenge for building robust, trustworthy, and rep [...]
22 July 14:40-15:00 (add to calendar)	04AB	Alisa Omelchenko	Network-based integration of epigenetic and transcriptomic landscapes unveils molecular programs underlying T follicular helper cell differentiation	CSI: Computational Systems Immunology	Using networks approaches allows us to integrate multi-modal datasets and view the immune system pathways with a multi-scale lens. Therefore, designin [...]
22 July 14:40-15:00 (add to calendar)	02F	Elmira Shajari	Mass Spectrometry and Machine Learning Reveal Stool-Based Multi-Signatures for Diagnosis and Longitudinal Monitoring of Inflammatory Bowel Disease	CompMS: Computational Mass Spectrometry	Background: Monitoring inflammation activity in Inflammatory Bowel Disease (IBD) is essential for guiding treatment and preventing long-term complica [...]
22 July 14:40-15:00 (add to calendar)	02F	Tom David Müller	Rapid Deployment of Interactive and Visual Web Applications for Computational Mass Spectrometry	CompMS: Computational Mass Spectrometry	Mass Spectrometry (MS) is a highly versatile bioanalytical technique with a myriad of experimental approaches, instrumentation, and computational tool [...]
22 July 14:40-15:00 (add to calendar)	11BC	Caroline Martiniuc	Antarctica as a Viral Reservoir: Insights from Comparative Genomics and Metagenomics	EvolCompGen: Evolution & Comparative Genomics	Two bioinformatics approaches stand out in the study of viromes in extreme environments: prophage comparative genomics and viral metagenomic analyses. [...]
22 July 14:40-15:00 (add to calendar)	12	Rund Tawfiq	On the completeness, coherence, and consistency of protein function prediction: lifting function prediction from isolated proteins to biological systems	Function: Gene and Protein Function Annotation	The Critical Assessment of Functional Annotation (CAFA) defines protein function prediction as the task of assigning Gene Ontology (GO) terms to indiv [...]
22 July 14:40-15:00 (add to calendar)	01A	Euxhen Hasanaj	Recovering Time-Varying Networks From Single-Cell Data	MLCSB: Machine Learning in Computational and Systems Biology	Gene regulation is a dynamic process that underlies all aspects of human development, disease response, and other key biological processes. The recons [...]
22 July 14:40-15:00 (add to calendar)	01B	Kivilcim Ozturk	Uncovering the systems-level mutational landscape of intrinsically disordered regions in cancer	NetBio: Network Biology	Biological functions and cellular behaviors arise from interactions among proteins and other molecules within cells, and cancers often act to perturb [...]
22 July 14:40-15:00 (add to calendar)	01C	Arnau Montagud	A community benchmark of off-lattice multiscale modelling tools reveals differences in methods and across-scales integrations	SysMod: Computational Modeling of Biological Systems	The emergence of virtual human twins (VHT) in biomedical research has sparked interest in multiscale modelling frameworks, particularly in their appli [...]
22 July 14:40-15:00 (add to calendar)	11A	Tim Kucera	The Bioverse - Biomolecule data processing for AI made easy	Tech Track	We introduce the bioverse, a free and open-source Python package that streamlines biological data preparation for machine learning. Focused on structu [...]
22 July 14:40-15:00 (add to calendar)	02N	Philip Kenneweg	Generating Synthetic Genotypes using Diffusion Models	TransMed: Translational Medicine Informatics & Applications	In this paper, we introduce the first diffusion model designed to generate complete synthetic human genotypes, which, by standard protocols, one can s [...]
22 July 14:50-15:00 (add to calendar)	03B	Javier Sánchez Utgés	Computational methods for the characterisation and evaluation of protein-ligand binding sites	3DSIG: Structural Bioinformatics and Computational Biophysics	Fragment screening is used for hit identification in drug discovery, but it is often unclear which binding sites are functionally relevant. Here, data [...]
22 July 15:00-15:20 (add to calendar)	03B	Alex Morehead	FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction	3DSIG: Structural Bioinformatics and Computational Biophysics	Motivation: Powerful generative models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein [...]
22 July 15:00-15:20 (add to calendar)	03A	Nick Juty	Applications of Bioschemas in FAIR, AI and knowledge representation	BOKR: Bio-Ontologies and Knowledge Representation	Bioschemas.org defines domain-specific metadata schemas based on schema.org extensions, which expose key metadata properties from resource records. Th [...]
22 July 15:00-15:20 (add to calendar)	03A	Nick Juty	Applications of Bioschemas in FAIR, AI and knowledge representation	BOSC: Bioinformatics Open Source Conference	Bioschemas.org defines domain-specific metadata schemas based on schema.org extensions, which expose key metadata properties from resource records. Th [...]
22 July 15:00-15:20 (add to calendar)	04AB	Isabella Withnell	Tissue first single cell RNA seq strategy reveals renal tumour specific expansion of regulatory DN1 B cells	CSI: Computational Systems Immunology	Pan cancer atlases often integrate cells across tissues, obscuring context specific immune states. We developed a tissue first single cell RNA seq pip [...]
22 July 15:00-15:20 (add to calendar)	02F	Zixuan Xiao	PepSi-Print: Unraveling Protein Fingerprints through Pairwise Intensity Ratios with a Peptide Siamese Network	CompMS: Computational Mass Spectrometry	In MS-based bottom-up proteomics, proteins are enzymatically digested into peptides, and identified and quantified to infer proteins. While MS2 spectr [...]
22 July 15:00-15:10 (add to calendar)	11BC	Milana Frenkel-Morgenstern	Computational Genomics and Biosynthetic Potential Analysis of a Dead Sea Penicillium sp.	EvolCompGen: Evolution & Comparative Genomics	Extreme environments harbor unique microbial life with biotechnological potential. Here, we characterize a novel Penicillium sp. isolated from the hyp [...]
22 July 15:00-15:20 (add to calendar)	12	Chih-Hsuan Wei	Contextual Gene Set Analysis with Large Language Models	Function: Gene and Protein Function Annotation	Gene set analysis (GSA) is a foundational technique in genomics research, enabling the identification of biological processes and disease mechanisms a [...]
22 July 15:00-15:10 (add to calendar)	01A	Jishnu Das	Sliding Window INteraction Grammar (SWING): a generalized interaction language model for peptide and protein interactions	MLCSB: Machine Learning in Computational and Systems Biology	Protein language models (pLMs) can embed protein sequences for different proteomic tasks. However, these methods are suboptimal at learning the langua [...]
22 July 15:00-15:20 (add to calendar)	01B	Erik Sonnhammer	Advancing Network Biology with FunCoup 6	NetBio: Network Biology	We recently released FunCoup 6, a major update to the FunCoup network database, providing researchers with a significantly improved and redesigned pla [...]
22 July 15:00-15:20 (add to calendar)	01C	Nhung Duong	Multi-objective Reinforcement Learning for Optimizing JAK/STAT Pathway Interventions: A Quantitative System Pharmacology Study	SysMod: Computational Modeling of Biological Systems	Background and Aims: JAK/STAT cancer pathway-oriented treatment optimization poses challenges due to pathway complexity, feedback loops, resistance de [...]
22 July 15:00-15:20 (add to calendar)	11A	Alberto Pepe	Data, We Need to Chat	Tech Track	"The exponential growth of biomedical datasets presents unprecedented opportunities for scientific discovery, yet researchers struggle to find and exp [...]
22 July 15:00-15:20 (add to calendar)	02N	Jian Liu	Predicting fine-grained cell types from histology images through cross-modal learning in spatial transcriptomics	TransMed: Translational Medicine Informatics & Applications	Motivation: Fine-grained cellular characterization provides critical insights into biological processes, including tissue development, disease progres [...]
22 July 15:10-15:20 (add to calendar)	11BC	Dr. Karan Kumar	Unravelling the pangenome of autotrophic bacteria: Metabolic commonalities, evolutionary relationships, and industrially relevant traits	EvolCompGen: Evolution & Comparative Genomics	Atmospheric CO₂ fixation by microbial autotrophs presents a sustainable alternative to energy-intensive chemical processes, offering significant poten [...]
22 July 15:10-15:20 (add to calendar)	01A	Gerold Csendes	Benchmarking foundation cell models for post-perturbation RNA-seq prediction	MLCSB: Machine Learning in Computational and Systems Biology	Accurately predicting cellular responses to perturbations is essential for understanding cell behaviour in both healthy and diseased states. While per [...]
22 July 15:20-15:40 (add to calendar)	03B	Alessia David	Mapping and characterization of the human missense variation universe using AlphaFold 3D models	3DSIG: Structural Bioinformatics and Computational Biophysics	The deep learning algorithm AlphaFold has revolutionized the field of structural biology by producing highly accurate three-dimensional models of the [...]
22 July 15:20-15:40 (add to calendar)	03A	Phil Reed	RO-Crate: Capturing FAIR research outputs in bioinformatics and beyond	BOKR: Bio-Ontologies and Knowledge Representation	RO-Crate is a mechanism for packaging research outputs with structured metadata, providing machine-readability and reproducibility following the FAIR [...]
22 July 15:20-15:40 (add to calendar)	03A	David Gordon	PheBee: A Graph-Based System for Scalable, Traceable, and Semantically Aware Phenotyping	BOKR: Bio-Ontologies and Knowledge Representation	The association of phenotypes and disease diagnoses is a cornerstone of clinical care and biomedical research. Significant work has gone into standard [...]
22 July 15:20-15:40 (add to calendar)	03A	Damien Goutte-Gattat	The role of the Ontology Development Kit in supporting ontology compliance in adverse legal landscapes	BOKR: Bio-Ontologies and Knowledge Representation	Ontologies, like code, are a form of speech. As such, they can be subject to laws and other regulations that attempt to control how freedom of speech [...]
22 July 15:20-15:40 (add to calendar)	03A	Phil Reed	RO-Crate: Capturing FAIR research outputs in bioinformatics and beyond	BOSC: Bioinformatics Open Source Conference	RO-Crate is a mechanism for packaging research outputs with structured metadata, providing machine-readability and reproducibility following the FAIR [...]
22 July 15:20-15:40 (add to calendar)	03A	David Gordon	PheBee: A Graph-Based System for Scalable, Traceable, and Semantically Aware Phenotyping	BOSC: Bioinformatics Open Source Conference	The association of phenotypes and disease diagnoses is a cornerstone of clinical care and biomedical research. Significant work has gone into standard [...]
22 July 15:20-15:40 (add to calendar)	03A	Damien Goutte-Gattat	The role of the Ontology Development Kit in supporting ontology compliance in adverse legal landscapes	BOSC: Bioinformatics Open Source Conference	Ontologies, like code, are a form of speech. As such, they can be subject to laws and other regulations that attempt to control how freedom of speech [...]
22 July 15:20-15:40 (add to calendar)	04AB	Dongjun Guo	ImmunoMatch learns and predicts cognate pairing of heavy and light immunoglobulin chains	CSI: Computational Systems Immunology	The development of stable antibodies formed by compatible heavy (H) and light (L) chain pairs is crucial in both the in vivo maturation of antibody-pr [...]
22 July 15:20-15:40 (add to calendar)	02F	Nicolas Provencher	Identification of novel proteins by integrating ribosome profiling data into a transcriptomic language model for deeper mass spectrometry analyses	CompMS: Computational Mass Spectrometry	Background – The human transcriptome contains millions of open reading frames (ORFeome) potentially coding for currently unknown or unannotated protei [...]
22 July 15:20-15:40 (add to calendar)	02F	Ceder Dens	Zero-shot retention time prediction for unseen post-translational modifications with molecular structure encodings	CompMS: Computational Mass Spectrometry	Identifying proteoforms with diverse post-translational modifications (PTMs) remains challenging in mass spectrometry-based proteomics. PTMs regulate [...]
22 July 15:20-15:30 (add to calendar)	11BC	Falk Hildebrand	Spatiotemporal patterns in the human gut dysbiosis contrasted to healthy families	EvolCompGen: Evolution & Comparative Genomics	The gut microbiome is essential to the wellbeing and health of its human host, yet most studies to date resolve the gut microbial community only at ge [...]
22 July 15:20-15:40 (add to calendar)	12	Harsh Srivastava	Fine-tuning protein language models with a disorder-aware vocabulary improves intrinsic disorder classification and function prediction	Function: Gene and Protein Function Annotation	Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are essential to cellular processes but lack stable 3D conformati [...]
22 July 15:20-15:30 (add to calendar)	01A	Jeremie Kalfon	scPRINT: pre-training on 50 million cells allows robust gene network predictions	MLCSB: Machine Learning in Computational and Systems Biology	A cell is governed by the interaction of myriads of macromolecules. Inferring such a network of interactions has remained an elusive milestone in cell [...]
22 July 15:20-15:40 (add to calendar)	01B	Dewei Hu	SPACE: STRING proteins as complementary embeddings	NetBio: Network Biology	Representation learning has revolutionized sequence-based prediction of protein function and subcellular localization. Protein networks are an importa [...]
22 July 15:20-15:40 (add to calendar)	01C	Bi-Rong Wang	Decoding CXCL9 regulatory mechanisms by integrating perturbation screenings with active learning of mechanistic logic-ODE models	SysMod: Computational Modeling of Biological Systems	Despite advances in immunotherapy, pancreatic cancer remains highly lethal due to an immunosuppressive tumor microenvironment characterized by immune [...]
22 July 15:20-15:40 (add to calendar)	11A	Zheng Chen	BioInfore: A No-Code Genome Data Management System Based On AI Agents	Tech Track	In many genomic projects, selecting and preparing assemblies requires complex database queries, manual metadata curation, and bespoke code scripting. [...]
22 July 15:20-15:40 (add to calendar)	02N	Hatice Osmanbeyoglu	Spatial Regulatory Landscape of the Glioblastoma Tumor Immune Microenvironment	TransMed: Translational Medicine Informatics & Applications	Glioblastoma (GBM) is the most aggressive primary brain tumor, with poor prognosis and limited treatment options. Its tumor microenvironment (TME) pla [...]
22 July 15:30-15:40 (add to calendar)	11BC	Beatriz Vieira Mourato	Marker discovery in the large	EvolCompGen: Evolution & Comparative Genomics	Pathogen outbreaks are now routinely tracked by whole genome sequencing. This leads to ever-increasing opportunities for marker discovery beyond the t [...]
22 July 15:30-15:40 (add to calendar)	01A	Hongmin Cai	MGCL-ST: Multi-view Graph Self-supervised Contrastive Learning for Spatial Transcriptomics Enhancement	MLCSB: Machine Learning in Computational and Systems Biology	Spatial transcriptomics enables the investigation of gene expression within its native spatial context, but existing technologies often suffer from lo [...]
22 July 15:40-16:00 (add to calendar)	03B	Guanglei Yu	CATH-ddG: towards robust mutation effect prediction on protein–protein interactions out of CATH homologous superfamily	3DSIG: Structural Bioinformatics and Computational Biophysics	Motivation: Protein-protein interactions (PPIs) are fundamental aspects in understanding biological processes. Accurately predicting the effects of mu [...]
22 July 15:40-16:00 (add to calendar)	03A	Robert Hoehndorf	10 years of the AberOWL ontology repository: moving towards federated reasoning and natural language access	BOKR: Bio-Ontologies and Knowledge Representation	AberOWL is a framework for ontology-based data access in biology that has provided reasoning services for bio-ontologies since 2015. Unlike other onto [...]
22 July 15:40-16:00 (add to calendar)	03A	Robert Hoehndorf	10 years of the AberOWL ontology repository: moving towards federated reasoning and natural language access	BOSC: Bioinformatics Open Source Conference	AberOWL is a framework for ontology-based data access in biology that has provided reasoning services for bio-ontologies since 2015. Unlike other onto [...]
22 July 15:40-16:00 (add to calendar)	04AB	Felipe Campelo	Taxon-specific linear B-cell epitope prediction with phylogeny-aware transfer learning	CSI: Computational Systems Immunology	The identification of linear B-cell epitopes (LBCEs) is an important step in the development of immunodiagnostic tests and vaccines. Most existing com [...]
22 July 15:40-16:00 (add to calendar)	02F	Valeriia Vasylieva	Open modification proteogenomics fosters reproducible detection of non-canonical proteins	CompMS: Computational Mass Spectrometry	MS-based proteomics enables the identification of thousands of proteins within a single sample. Analysis of MS/MS spectra involves database search eng [...]
22 July 15:40-16:00 (add to calendar)	02F	Steffen Lemke	PCI-DB: A novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development	CompMS: Computational Mass Spectrometry	Various cancer immunotherapies rely on the T cell-mediated recognition of peptide antigens presented on human leukocyte antigens (HLA). However, the i [...]
22 July 15:40-15:50 (add to calendar)	11BC	Ercan Seçkin	Whole-genome detection and origin identification of orphan genes in plant-parasitic nematodes	EvolCompGen: Evolution & Comparative Genomics	Genes with no known homologs constitute 5% to 30% of every organism’s genome. These orphan genes have either rapidly diverged from a family or have ap [...]
22 July 15:40-15:50 (add to calendar)	12	Catherine Zhou	A Novel Computational Pipeline for the Functional Characterization and Deorphanization of G-Protein Coupled Receptors	Function: Gene and Protein Function Annotation	G protein-coupled receptors (GPCRs) are integral membrane proteins central to cellular signaling and intercellular communication, with Class A GPCRs p [...]
22 July 15:40-15:50 (add to calendar)	01A	Rafael dos Santos Peixoto	Characterizing cell-type spatial relationships across length scales in spatially resolved omics data	MLCSB: Machine Learning in Computational and Systems Biology	Spatially resolved omics (SRO) technologies enable the identification of cell types while preserving their organization within tissues. Application of [...]
22 July 15:40-16:00 (add to calendar)	01B	Beatriz Urda-García	Disentangling the genetic and non-genetic origin of disease co-occurrences	NetBio: Network Biology	Numerous diseases co-occur more than expected by chance, likely due to a combination of genetic and environmental factors. However, the extent to whic [...]
22 July 15:40-16:00 (add to calendar)	01C	Sayali Anil Alatkar	ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population and perturbation from time-series single-cell data	SysMod: Computational Modeling of Biological Systems	Cellular processes like development, differentiation, and disease progression are highly complex and dynamic (e.g., gene expression). These processes [...]
22 July 15:40-16:00 (add to calendar)	11A		Omi: Bridging the Informatics to Bio Gap with a Natural Language Co-pilot	Tech Track	Omi facilitates bioinformatics analysis by replacing complex command-line processes with a natural language bioinformatics co-pilot. We codify bioinfo [...]
22 July 15:40-15:50 (add to calendar)	02N	Shilin Zhao	SpatialPathomicsToolkit: A Comprehensive Framework for Pathomics Feature Analysis and Integration	TransMed: Translational Medicine Informatics & Applications	Abstract: We present SpatialPathomicsToolkit, a modular and platform-agnostic toolkit for comprehensive analysis of pathomics features from whole slid [...]
22 July 15:50-16:00 (add to calendar)	11BC	Isabella Gallego	Construction and Analysis of the Moniliophthora roreri pangenome	EvolCompGen: Evolution & Comparative Genomics	Moniliophthora roreri, the causal agent of frosty pod rot, is a devastating fungal pathogen affecting cacao production across Latin America. Its broad [...]
22 July 15:50-16:00 (add to calendar)	12	Jason McDermott	VaLPAS: Leveraging variation in experimental multi-omics data to elucidate protein function	Function: Gene and Protein Function Annotation	Despite continuing advances in sequencing and computational function determination, large parts of the studied gene, protein and metabolite space rema [...]
22 July 15:50-16:00 (add to calendar)	01A	Elyas Heidari	Segger: Fast and accurate cell segmentation of imaging-based spatial transcriptomics data	MLCSB: Machine Learning in Computational and Systems Biology	Accurate cell segmentation is a critical first step in the analysis of imaging-based spatial transcriptomics (iST). Despite decades of research in ce [...]
22 July 15:50-16:00 (add to calendar)	02N	Marcelo Hurtado	CellTFusion: A novel approach to unravel cell states via cell type deconvolution and TF activity estimated from bulk RNAseq data identifies clinically relevant cell niches	TransMed: Translational Medicine Informatics & Applications	The tumor microenvironment (TME) plays a key role in cancer development by influencing physiopathological processes. Despite significant progress in u [...]
22 July 16:40-17:00 (add to calendar)	03B	Raymund Hackett	Investigating Enzyme Function by Geometric Matching of Catalytic Motifs	3DSIG: Structural Bioinformatics and Computational Biophysics	Detecting catalytic features in protein structures can provide important hints about enzyme function and mechanism. Keeping pace with the rapidly grow [...]
22 July 16:40-16:50 (add to calendar)	03A	Guy Cochrane	The global biodata infrastructure: how, where, who, and what?	BOKR: Bio-Ontologies and Knowledge Representation	Life science and biomedical research around the world is critically dependent on a global infrastructure of biodata resources that store and provide a [...]
22 July 16:40-16:50 (add to calendar)	03A	Guy Cochrane	The global biodata infrastructure: how, where, who, and what?	BOSC: Bioinformatics Open Source Conference	Life science and biomedical research around the world is critically dependent on a global infrastructure of biodata resources that store and provide a [...]
22 July 16:40-17:00 (add to calendar)	04AB	Pengfei Zhang	Iterative Attack-and-Defend Framework for Improving TCR-Epitope Binding Prediction Models	CSI: Computational Systems Immunology	Reliable TCR-epitope binding prediction models are essential for development of adoptive T cell therapy and vaccine design. These models often struggl [...]
22 July 16:40-17:00 (add to calendar)	02F	Lucas Miranda	CellPick: a cell selection toolkit for spatial proteomics	CompMS: Computational Mass Spectrometry	We present CellPick: a computational tool for facilitating the selection of cells for laser microdissection in spatial proteomics applications. Laser [...]
22 July 16:40-17:00 (add to calendar)	11BC	Yuan Wei	Recomb-Mix: fast and accurate local ancestry inference	EvolCompGen: Evolution & Comparative Genomics	Motivation: The availability of large genotyped cohorts brings new opportunities for revealing the high-resolution genetic structure of admixed popula [...]
22 July 16:40-17:00 (add to calendar)	12	Matthias Blum	Accelerating protein family classification in InterPro with AI innovations	Function: Gene and Protein Function Annotation	InterPro is a freely accessible resource for classifying protein sequences into families, domains, and functional sites, integrating predictive signat [...]
22 July 16:40-16:50 (add to calendar)	01A	Aarthi Venkat	Dissecting cellular and molecular mechanisms of pancreatic cancer with deep learning	MLCSB: Machine Learning in Computational and Systems Biology	Pancreatic endocrine-exocrine crosstalk plays a key role in normal physiology and disease and is perturbed by altered host metabolic states. For examp [...]
22 July 16:40-17:00 (add to calendar)	01B	Lucas Gillenwater	GRACKLE: An interpretable matrix factorization approach for biomedical representation learning	NetBio: Network Biology	Motivation: Disruption in normal gene expression can contribute to the development of diseases and chronic conditions. However, identifying disease-sp [...]
22 July 16:40-17:00 (add to calendar)	01C	Ati Ahmadi	Calibrating agent‐based models of colicin-mediated inhibition in microfluidic traps using single-cell time-lapse microscopy	SysMod: Computational Modeling of Biological Systems	I uploaded the long abstract below. [...]
22 July 16:40-17:00 (add to calendar)	11A		Introducing the Longitude Prize on ALS	Tech Track	The Longitude Prize on ALS is a £7.5m [~$10m USD] international programme that seeks to incentivise the use of AI-based approaches to transform therap [...]
22 July 16:40-16:50 (add to calendar)	02N	Satoko Namba	TRESOR: a disease signature integrating GWAS and TWAS for therapeutic target discovery in rare diseases	TransMed: Translational Medicine Informatics & Applications	Identifying therapeutic targets for diseases is important in drug discovery. However, the depletion of viable therapeutic targets has a major bottlene [...]
22 July 16:50-17:50 (add to calendar)	03A		Data Sustainability	BOKR: Bio-Ontologies and Knowledge Representation	This BOSC 2025 panel will tackle the essential challenge of Data Sustainability, defined as the proactive and principled approach to ensuring bioinfor [...]
22 July 16:50-17:50 (add to calendar)	03A		Data Sustainability	BOSC: Bioinformatics Open Source Conference	This BOSC 2025 panel will tackle the essential challenge of Data Sustainability, defined as the proactive and principled approach to ensuring bioinfor [...]
22 July 16:50-17:00 (add to calendar)	01A	Yuna Miyachi	SpliceSelectNet: A Hierarchical Transformer-Based Deep Learning Model for Splice Site Prediction	MLCSB: Machine Learning in Computational and Systems Biology	RNA splicing is a critical post-transcriptional process that enables the generation of diverse protein isoforms. Aberrant splicing is implicated in a [...]
22 July 16:50-17:00 (add to calendar)	02N	Peter White	GENIUS: Genomic Evaluation using Next-generation Intelligence for Understanding & Swift Diagnosis	TransMed: Translational Medicine Informatics & Applications	More than 350 million individuals globally suffer from approximately 10,000 known rare diseases. Despite genomic advances, patients today experience p [...]
22 July 17:00-17:20 (add to calendar)	03B	Gyorgy Abrusan	Cellular location shapes quaternary structure of enzymes.	3DSIG: Structural Bioinformatics and Computational Biophysics	The main forces driving protein complex evolution are currently not well understood, especially in homomers, where quaternary structure might frequent [...]
22 July 17:00-17:20 (add to calendar)	04AB	Ko-Han Lee	NeoPrecis: A Computational Framework for Assessing Neoantigen Immunogenicity to Advance Cancer Immunotherapy	CSI: Computational Systems Immunology	Cancer immunotherapy, including immune checkpoint inhibitors (ICIs) and personalized cancer vaccines, has transformed cancer treatment. However, respo [...]
22 July 17:00-17:20 (add to calendar)	02F	Marina Pominova	A living proteomics benchmark for comprehensive evaluation of deep learning-based de novo peptide sequencing tools	CompMS: Computational Mass Spectrometry	Mass spectrometry-based proteomics is essential for understanding protein composition and function, yet traditional sequence database-based methods fa [...]
22 July 17:00-17:20 (add to calendar)	02F		Mavis: An Ensemble of Methods for Mean-Variance Trend Modeling and Bayesian Decision in Comparative Proteomics	CompMS: Computational Mass Spectrometry	Motivation: Comparative methods that use dataset-level information such as mean-variance have been highly successful for several types of -omics data. [...]
22 July 17:00-17:20 (add to calendar)	11BC	Hannah Snell	WINDEX: A hierarchical integration of site- and window-based statistics for modeling the footprint of positive selection	EvolCompGen: Evolution & Comparative Genomics	In genetics studies, scientists search for mutations that explain changes in phenotype or population diversity. Adaptive mutations, or mutations that [...]
22 July 17:00-17:20 (add to calendar)	12	Simon Jeanneau	Thousands of confident genetic interactions in an Escherichia coli mutant collection elucidate numerous gene functions	Function: Gene and Protein Function Annotation	Despite extensive research, nearly one-third of Escherichia coli genes remain uncharacterized. Understanding how these genes interact to support cellu [...]
22 July 17:00-18:00 (add to calendar)	01A	Sanmi Koyejo	Is distribution shift still an AI problem	MLCSB: Machine Learning in Computational and Systems Biology	Distribution shifts describe the phenomena where the deployment performance of an AI model exhibits differences from training. On the one hand, some c [...]
22 July 17:00-17:20 (add to calendar)	01B	Aritra Bose	Quantum Random Walks for Biomarker Discovery in Biomolecular Networks	NetBio: Network Biology	Biomolecular networks, such as protein–protein interactions, gene–gene associations, and cell–cell interactions, offer valuable insights into the comp [...]
22 July 17:00-17:20 (add to calendar)	01C	Erick Armingol	Inferring metabolic activities from single-cell and spatial transcriptomic atlases	SysMod: Computational Modeling of Biological Systems	Metabolism is fundamental to cellular function, supporting macromolecule synthesis, signaling, growth, and cell-cell communication. While single-cell [...]
22 July 17:00-17:10 (add to calendar)	02N	Yasmin Jolasun	SIDISH Identifies High-Risk Disease-Associated Cells and Biomarkers by Integrating Single-Cell Depth and Bulk Breadth	TransMed: Translational Medicine Informatics & Applications	Single-cell RNA sequencing (scRNA-seq) offers unparalleled resolution for studying cellular heterogeneity but is costly, restricting its use to small [...]
22 July 17:10-17:50 (add to calendar)	02N	Jonathan Carlson	The Emergence of General AI in Biomedicine	TransMed: Translational Medicine Informatics & Applications	The fundamental breakthrough of generative AI is the ability to automatically learn, extract, express, and reason over concepts. And not just concepts [...]
22 July 17:20-17:40 (add to calendar)	03B	Gabriel Cia	In silico design of stable single-domain antibodies with high affinity	3DSIG: Structural Bioinformatics and Computational Biophysics	Monoclonal antibodies are rapidly becoming a standard drug format in the pharmaceutical industry, but current immunization-based methods for antibody [...]
22 July 17:20-17:40 (add to calendar)	04AB	Antonio Collesei	SHISMA: Shape-driven inference of significant celltype-specific subnetworks from time series single-cell transcriptomics	CSI: Computational Systems Immunology	Recent advances in RNA sequencing technologies and the gradual decrease in costs have allowed to design serial experiments with time embeddings, even [...]
22 July 17:20-18:00 (add to calendar)	02F	Tine Claeys	Making Proteomics AI-Ready: From Metadata Extraction to Biomarker Discovery	CompMS: Computational Mass Spectrometry	Public proteomics repositories from ProteomeXchange hold a vast, largely untapped resource for biological discovery. However, reuse of public proteomi [...]
22 July 17:20-17:30 (add to calendar)	11BC	Pavitra Selvakumar	Position-specific evolution in transcription factor binding sites, and a fast likelihood calculation for the F81 model	EvolCompGen: Evolution & Comparative Genomics	Transcription factor binding sites (TFBS), like other DNA sequence, evolve via mutation and selection relating to their function. Models of nucleotide [...]
22 July 17:20-17:40 (add to calendar)	12	M. Clara De Paolis Kaluza	Present and future of the critical assessment of protein function annotation algorithms (CAFA)	Function: Gene and Protein Function Annotation	Since its launch in 2010, the Critical Assessment of Functional Annotation (CAFA) has brought together computational biologists, biocurators, and expe [...]
22 July 17:20-18:00 (add to calendar)	01B	Jan Baumbach	Quantum computing for network medicine-based epistatic disease mechanism mining - Fake it till you make it?	NetBio: Network Biology	Most heritable diseases are polygenic and yield complex disease mechanisms. To comprehend the underlying genetic architecture, it is crucial to discov [...]
22 July 17:20-17:40 (add to calendar)	01C	Koichiro Majima	Spatiotemporal Variational Autoencoders for Continuous Single-Cell Tissue Dynamics	SysMod: Computational Modeling of Biological Systems	Single-cell spatial genomics provides unprecedented molecular insights, yet it still struggles to track both the spatial and temporal progression of t [...]
22 July 17:30-18:00 (add to calendar)	11BC		Concluding remarks	EvolCompGen: Evolution & Comparative Genomics
22 July 17:40-18:00 (add to calendar)	03B	Rakshanda Sajeed	An improved deep learning model for immunogenic B epitope prediction	3DSIG: Structural Bioinformatics and Computational Biophysics	The recognition of B epitopes by B cells of the immune system initiates immune response that leads to production of antibodies to combat bacterial and [...]
22 July 17:40-17:45 (add to calendar)	04AB	Divya Sitani	Unraveling Immune Signatures of Whole-Cell vs. Acellular Pertussis Vaccine Priming through Multi-Omics Feature Fusion	CSI: Computational Systems Immunology	Early life vaccination with whole cell or acellular pertussis vaccines shapes long term immune trajectories that influence responses to booster immuni [...]
22 July 17:40-18:00 (add to calendar)	12	Erva Ulusoy	ProtHGT: Heterogeneous Graph Transformers for Automated Protein Function Prediction Using Biological Knowledge Graphs and Language Models	Function: Gene and Protein Function Annotation	Accurate functional annotation of proteins is crucial for understanding complex biological systems. As protein sequence data grows rapidly, experiment [...]
22 July 17:40-17:45 (add to calendar)	01C	Marek Kimmel	Computational Modeling of Shortening and Reconstruction of Telomeres	SysMod: Computational Modeling of Biological Systems	We discuss a stochastic model of growth of a cell population of cultured yeast cells with gradually decaying chromosome endings called the telomeres, [...]
22 July 17:45-17:50 (add to calendar)	04AB	Bünyamin Şen	BepiCon: A Geometric Deep Learning Framework for Conformational B Cell Epitope Prediction	CSI: Computational Systems Immunology	Accurate and reliable prediction of B cell epitopes holds critical importance in immunology and vaccine development. While traditional experimental me [...]
22 July 17:45-17:50 (add to calendar)	01C	Jiachen Li	TFvelo: gene regulation inspired RNA velocity estimation	SysMod: Computational Modeling of Biological Systems	RNA velocity is closely related with cell fate and is an important indicator for the prediction of cell states with elegant physical explanation deriv [...]
22 July 17:50-18:00 (add to calendar)	03A		Closing Remarks	BOKR: Bio-Ontologies and Knowledge Representation
22 July 17:50-18:00 (add to calendar)	03A		Closing Remarks	BOSC: Bioinformatics Open Source Conference
22 July 17:50-17:55 (add to calendar)	04AB	Jonas Schuck	NanoAIRR: full-length adaptive immune receptor profiling from Nanopore long-read sequencing	CSI: Computational Systems Immunology	Characterizing the antigen receptor repertoire of adaptive immune cells in solid tumors is essential for understanding the dynamics of immune response [...]
22 July 17:50-18:00 (add to calendar)	01C		Closing remarks	SysMod: Computational Modeling of Biological Systems	This concluding talk aims to briefly discuss the diversity of topics presented at the “Computational Modeling of Biological Systems” (SysMod) COSI tra [...]
22 July 18:00-19:30 (add to calendar)	-		Success Circles - Reinvented Networking where participants are grouped into small circles, each led by a knowledgeable facilitator	Special Track
23 July 08:40-09:00 (add to calendar)	01A	-	Morning Welcome and Keynote Introduction	Distinguished Keynotes
23 July 09:00-10:00 (add to calendar)	01A	Charlotte Deane	Building the future of AI-driven structure-based drug discovery	Distinguished Keynotes	The development of new therapeutics typically takes many years and requires over $1bn in investment. Computational methods and in particular, machine [...]
23 July 11:20-11:40 (add to calendar)	03A	Marcin Joachimiak	Knowledge-Graph-driven and LLM-enhanced Microbial Growth Predictions	BOKR: Bio-Ontologies and Knowledge Representation	Predicting microbial growth preferences has far-reaching impacts in biotechnology, healthcare, and environmental management. Cultivating microbes allo [...]
23 July 11:20-12:00 (add to calendar)	04AB	Damian Dalle Nogare	Bioimage analysis in the age of AI: lessons and a path forward from a core facility perspective.	BioInfo-Core	In recent years, much of the toolchain used in advanced bioimage analysis has become dominated by approaches relying on deep learning/artificial intel [...]
23 July 11:20-12:20 (add to calendar)	01C	Thomas Rattei	Genome-based prediction of microbial traits	CAMDA: Critical Assessment of Massive Data Analysis	The prediction of phenotypic traits from genomic information is an ongoing challenge in computational biology. Although the fundamental principles of [...]
23 July 11:20-13:00 (add to calendar)	02F		CollaborationFest	CollaborationFest
23 July 11:20-11:40 (add to calendar)	12	Lynn Schriml	Disease Ontology Knowledgebase: A Global BioData hub for FAIR disease data discovery	ELIXIR/NIH-ODSS	Development of long-term biodata resources, by design, depends on a stable data model with persistent identifiers, regular data releases, and reliable [...]
23 July 11:20-12:00 (add to calendar)	11A	Gabriela Rustici	Cross-Sector Collaboration in Bioinformatics and Data Science: Tackling Skill Development Challenges in Academia and Industry	Education: Computational Biology and Bioinformatics Education and Training	The rapid evolution of bioinformatics and data science has created shared challenges for both academia and industry, particularly in developing essent [...]
23 July 11:20-12:20 (add to calendar)	01A	Valentina Boeva	Learning variant effects on chromatin accessibility and 3D structure without matched Hi-C data	HiTSeq: High Throughput Sequencing Algorithms & Applications	Chromatin interactions provide insights into which DNA regulatory elements connect with specific genes, informing the activation or repression of gene [...]
23 July 11:20-11:40 (add to calendar)	03B		Opening Remarks & Framing the Ecosystem	Innovation at the Intersection: Industry's Role in Bioinformatics	• Introduction of the ISCB Industry Advisory Council and session overview • Overview of the academia–industry–startup pipeline • Framing questions: Ho [...]
23 July 11:20-11:40 (add to calendar)	01B	Dongmin Bang	MixingDTA: Improved Drug-Target Affinity Prediction by Extending Mixup with Guilt-By-Association	NetBio: Network Biology	Drug–Target Affinity (DTA) prediction is an important regression task for drug discovery, which can provide richer information than traditional drug-t [...]
23 July 11:20-12:00 (add to calendar)	11BC	Vera Pancaldi	Exploring cellular plasticity: 4D epigenomes in the context of the tumour microenvironment	RegSys: Regulatory and Systems Genomics	Oncogenesis is characterized by alterations in chromatin organization and the reactivation of unicellular phenotypes at both metabolic and transcripti [...]
23 July 11:20-11:30 (add to calendar)	02N		Introduction to iRNA	iRNA: Integrative RNA Biology
23 July 11:30-12:10 (add to calendar)	02N	Steven West	Sequential verification of transcription by Integrator and Restrictor	iRNA: Integrative RNA Biology	The decision between productive elongation and premature termination of promoterproximal RNA polymerase II (RNAPII) is fundamental to metazoan gene re [...]
23 July 11:40-12:00 (add to calendar)	03A	Jovana Kovacevic	ProDiGenIDB – a unified resource of disease-associated genes, their protein products, and intrinsic disorder annotations	BOKR: Bio-Ontologies and Knowledge Representation	Understanding gene-disease associations is essential in biomedical research, yet relevant information is often distributed across multiple heterogeneo [...]
23 July 11:40-12:00 (add to calendar)	12	Julia Koblitz	Integrating Data Treasures: Knowledge graphs of the DSMZ Digital Diversity	ELIXIR/NIH-ODSS	The DSMZ (German Collection of Microorganisms and Cell Cultures) hosts a wealth of biological data, covering microbial traits (BacDive), taxonomy (LPS [...]
23 July 11:40-12:00 (add to calendar)	03B		Startup Ecosystems & Translational Science	Innovation at the Intersection: Industry's Role in Bioinformatics	Explore the early stages of innovation where research meets entrepreneurship. Speakers will discuss: • What makes a scientific idea “translatable” in [...]
23 July 11:40-12:00 (add to calendar)	01B	Nicoleta Siminea	Interactome-based computational solutions to support personalized drug therapy decisions in glioblastoma	NetBio: Network Biology	Glioblastoma is an aggressive cancer with a poor survival rate, and standard treatments often yield limited results. To explore personalized treatment [...]
23 July 12:00-12:20 (add to calendar)	03A	Sumyyah Toonsi	Causal knowledge graph analysis identifies adverse drug effects	BOKR: Bio-Ontologies and Knowledge Representation	Motivation: Knowledge graphs and structural causal models have each proven valuable for organizing biomedical knowledge and estimating causal effects, [...]
23 July 12:00-13:00 (add to calendar)	04AB		The rise of computational imaging	BioInfo-Core	Thanks in part to the popularity of spatial transcriptomics, many of us are now being faced with challenges that can be helped or solved with imaging [...]
23 July 12:00-12:20 (add to calendar)	12	Mano Maurya	Metabolomics Workbench: Data Sharing, Analysis and Integration at the National Metabolomics Data Repository	ELIXIR/NIH-ODSS	The National Metabolomics Data Repository (NMDR) was developed as part of the National Institutes of Health (NIH) Common Fund Metabolomics Program to [...]
23 July 12:00-12:20 (add to calendar)	11A	Allissa Dillman	Building Omics Skills through the CFDE Training Center	Education: Computational Biology and Bioinformatics Education and Training	The Common Fund Data Ecosystem (CFDE) enables broad use of Common Fund data to advance scientific discovery. Five Centers integrate data, resources, a [...]
23 July 12:00-12:20 (add to calendar)	03B		Public-Private Partnerships and Career Navigation	Innovation at the Intersection: Industry's Role in Bioinformatics	Focus on later-stage collaborations and real-world applications. Panelists will cover: • How computational biology fuels industry R&D pipelines • Coll [...]
23 July 12:00-12:20 (add to calendar)	01B	Terence Egbelo	Improving Target-Adverse Event Association Prediction by Mitigating Topological Imbalance in Knowledge Graphs	NetBio: Network Biology	Drug discovery faces high clinical failure rates due to adverse events (AEs) from both on- and off-target interactions. Biomedical knowledge graphs (K [...]
23 July 12:00-12:20 (add to calendar)	11BC	Yijie Wang	Leveraging Transcription Factor Physical Proximity for Enhancing Gene Regulation Inference	RegSys: Regulatory and Systems Genomics	Motivation: Gene regulation inference, a key challenge in systems biology, is crucial for understanding cell function, as it governs processes such as [...]
23 July 12:10-12:20 (add to calendar)	02N	Yuan Gao	CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning	iRNA: Integrative RNA Biology	Circular RNAs (circRNAs) are a crucial yet relatively unexplored class of transcripts known for their tissue- and cell-type-specific expression patter [...]
23 July 12:20-12:40 (add to calendar)	03A	Erva Ulusoy	CROssBARv2: A Unified Biomedical Knowledge Graph for Heterogeneous Data Representation and LLM-Driven Exploration	BOKR: Bio-Ontologies and Knowledge Representation	Developing effective therapeutics against prevalent diseases requires a deep understanding of molecular, genetic, and cellular factors involved in dis [...]
23 July 12:20-12:40 (add to calendar)	01C	Leonid Chidelevitch	The Anti-Microbial Resistance Prediction Challenge - Introduction	CAMDA: Critical Assessment of Massive Data Analysis	The AMR prediction challenge at CAMDA is now in its third year. This year's challenge on predicting AMR quantiatively (MIC values) as well as qualitat [...]
23 July 12:20-12:40 (add to calendar)	12	Karamarie Fecho	Building sustainable solutions for federally-funded open-source biomedical tools and technologies	ELIXIR/NIH-ODSS	Federally-funded, open-source, biomedical tools and technologies often fail due to a lack of a business model for sustainability, which quickly leads [...]
23 July 12:20-12:40 (add to calendar)	11A	Ajay Mishra	From live webinar series to self-paced learning resource: Creating structured bioinformatics learning pathways	Education: Computational Biology and Bioinformatics Education and Training	As bioinformatics continues to advance and expand across life sciences research, learners often struggle to navigate complex topics without structured [...]
23 July 12:20-12:40 (add to calendar)	01A	Laura D. Martens	Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data	HiTSeq: High Throughput Sequencing Algorithms & Applications	Motivation: Spatially resolved chromatin accessibility profiling offers the potential to investigate gene regulatory processes within the spatial cont [...]
23 July 12:20-12:40 (add to calendar)	03B		Funding & Government Innovation Strategies	Innovation at the Intersection: Industry's Role in Bioinformatics	Review some key areas of funding strategy aligning with innovation pipelines such as: • Navigating government and cross-sector funding channels • Emer [...]
23 July 12:20-12:40 (add to calendar)	01B	Johannes Kersting	A Nextflow Pipeline for Network-Based Disease Module Identification and Drug Repurposing	NetBio: Network Biology	Disease modules provide unique insights into the mechanisms of complex diseases and lay the foundation for mechanistic drug repurposing. Algorithms fo [...]
23 July 12:20-12:40 (add to calendar)	11BC	Panagiotis Alexiou	miRBench: novel benchmark datasets for microRNA binding site prediction that mitigate against prevalent microRNA Frequency Class Bias	RegSys: Regulatory and Systems Genomics	Motivation: MicroRNAs (miRNAs) are crucial regulators of gene expression, but the precise mechanisms governing their binding to target sites remain un [...]
23 July 12:20-12:40 (add to calendar)	02N	Juseong Kim	Enhancing circRNA–miRNA Interaction Prediction with Structure-aware Sequence Modeling	iRNA: Integrative RNA Biology	Circular RNAs (circRNAs) function as key post-transcriptional regulators by interacting with microRNAs (miRNAs) to modulate gene expression. These int [...]
23 July 12:40-12:45 (add to calendar)	03A	Galadriel Brière	Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings	BOKR: Bio-Ontologies and Knowledge Representation	In recent years, Knowledge Graphs (KGs) have gained significant attention for their ability to organize massive biomedical knowledge into entities and [...]
23 July 12:40-13:00 (add to calendar)	01C	Anton Pashkov	A Hybrid Pipeline for Feature Reduction, and Ordinal Classification to Predict Antimicrobial Resistance from Genetic Profiles	CAMDA: Critical Assessment of Massive Data Analysis	One of the three challenges proposed by the Community of Interest Critical Assessment of Massive Data Analysis (CAMDA) involves predicting antimicrobi [...]
23 July 12:40-13:00 (add to calendar)	12	Yongqun He	SEA CDM: An Ontology-Based Common Data Model for Standardizing and Integrating Biomedical Experimental Data in Vaccine Research	ELIXIR/NIH-ODSS	With the increasing volume of experimental data across biomedical fields, standardizing, sharing, and integrating heterogeneous experimental data has [...]
23 July 12:40-13:00 (add to calendar)	11A	Dusanka Nikolic	Breaking Down Barriers to Learning: Bioinformatics for Biologists Massive Open Online Courses	Education: Computational Biology and Bioinformatics Education and Training	Background: To meet growing demand for training in core bioinformatics skills, we designed and delivered a free, two-part Massive Open Online Course ( [...]
23 July 12:40-13:00 (add to calendar)	01A	Tanmayee Narendra	Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays	HiTSeq: High Throughput Sequencing Algorithms & Applications	Epigenetic mechanisms enable cellular differentiation and the maintenance of distinct cell-types. They enable rapid responses to external signals thro [...]
23 July 12:40-13:00 (add to calendar)	03B		How Industry & Academia Can Work Together in Computational Biology:Panel Discussion	Innovation at the Intersection: Industry's Role in Bioinformatics
23 July 12:40-13:00 (add to calendar)	01B	Samuele Firmani	Graph Antiviral Target Explorer (GATE): predicting disease genes in viral infections with Message Passing Neural Networks	NetBio: Network Biology	Recent outbreaks of COVID‑19 and monkeypox (Mpox) underscore the need for scalable tools that can disentangle complex host‑virus‑drug interactions and [...]
23 July 12:40-13:00 (add to calendar)	11BC		Flash Talk Session 1	RegSys: Regulatory and Systems Genomics	Session with 4 short talks: Aryan Kamal - Transcriptional regulation of cell fate plasticity in hematopoiesis Damla Övek Baydar - Enhancing JASPAR a [...]
23 July 12:40-13:00 (add to calendar)	02N		Flash talks	iRNA: Integrative RNA Biology	1-minute flash talks advertising iRNA posters [...]
23 July 12:45-12:50 (add to calendar)	03A	Mun Su Kwon	A machine learning framework for extracting and structuring biological pathway knowledge from scientific literature	BOKR: Bio-Ontologies and Knowledge Representation	Advances in text mining have significantly improved the accessibility of scientific knowledge from literature. However, a major challenge in biology a [...]
23 July 12:50-13:00 (add to calendar)	03A		Poster Madness	BOKR: Bio-Ontologies and Knowledge Representation	Each accepted poster presenter is given up 1 minute to advertise their poster. [...]
23 July 14:00-14:20 (add to calendar)	03A	Yuyao Song	ScGOclust: leveraging gene ontology to find functionally analogous cell types between distant species	BOKR: Bio-Ontologies and Knowledge Representation	Basic biological processes are shared across animal species, yet their cellular mechanisms are profoundly diverse. Comparing cell-type gene expression [...]
23 July 14:00-15:00 (add to calendar)	04AB		The practical use of AI in cores	BioInfo-Core	It’s here and it’s being used. How do we use it to good effect, and how do we teach our collaborators to use it? This topic could include not only gen [...]
23 July 14:00-14:40 (add to calendar)	01C	Jack Vaska	Predicting Antimicrobial Resistance Using Microbiome-Pretrained DNABERT2 and DBGWAS-Derived Genomic Features	CAMDA: Critical Assessment of Massive Data Analysis	Antimicrobial resistance (AMR) is an escalating public health threat, especially in hospitals where diverse resistance gene reservoirs have emerged. W [...]
23 July 14:00-16:00 (add to calendar)	02F		CollaborationFest	CollaborationFest
23 July 14:00-14:20 (add to calendar)	12	Mallory Freeberg	The Evolution of Ensembl: Scaling for Accessibility, Performance, and Interoperability	ELIXIR/NIH-ODSS	Ensembl is an open platform that integrates publicly available genomics data across the tree of life, enabling activities spanning research to clinica [...]
23 July 14:00-14:20 (add to calendar)	11A	Farzana Rahman	An educator framework for organizing Wikipedia editathons for computational biology	Education: Computational Biology and Bioinformatics Education and Training	Motivation Wikipedia is a vital open educational resource in computational biology; however, a significant knowledge gap exists between English and No [...]
23 July 14:00-14:20 (add to calendar)	01A	Noor Pratap Singh	Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-Seq data using virtual colors for accurate genomic pseudoalignment	HiTSeq: High Throughput Sequencing Algorithms & Applications	Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenom [...]
23 July 14:00-14:20 (add to calendar)	01B	Piotr Sliwa	Multilayer Networks Identify Clinically Relevant Patient Endotypes in COVID-19 and Sepsis	NetBio: Network Biology	Integrative analyses of multi-omic patient datasets are crucial to uncover disease subtypes, yet challenges arise from modality‑specific variability a [...]
23 July 14:00-14:20 (add to calendar)	11BC	Oluwatosin Oluwadare	Unicorn: Enhancing Single-Cell Hi-C Data with Blind Super-Resolution for 3D Genome Structure Reconstruction	RegSys: Regulatory and Systems Genomics	Motivation: Single-cell Hi-C (scHi-C) data provide critical insights into chromatin interactions at individual cell levels, uncovering unique genomic [...]
23 July 14:00-14:20 (add to calendar)	02N	Étienne Fafard-Couture	Predicting relevant snoRNA genes across any eukaryote genome using SnoBIRD	iRNA: Integrative RNA Biology	Small nucleolar RNAs (snoRNAs) are a group of noncoding RNAs identified in all eukaryotes. In human, C/D box snoRNAs are the most prevalent class, dis [...]
23 July 14:20-14:40 (add to calendar)	03A	Fabien Maury	Integrating autoantibody-related knowledge in an ontology populated using a curated dataset from literature	BOKR: Bio-Ontologies and Knowledge Representation	Autoimmune diseases (AIDs) are often characterized by the presence of autoantibodies (AAbs). But many of these diseases are rare and can be hard to di [...]
23 July 14:20-14:40 (add to calendar)	12	Kate Warner	Insights from GlyGen in Developing Sustainable Knowledgebases with Well-Defined Infrastructure Stacks	ELIXIR/NIH-ODSS	GlyGen is a data integration and dissemination project for glycan and glycoconjugate related data, which retrieves information from multiple internati [...]
23 July 14:20-14:40 (add to calendar)	11A	Pavlin G. Poličar	Automated Assignment Grading with Large Language Models: Insights From a Bioinformatics Course	Education: Computational Biology and Bioinformatics Education and Training	Providing students with individualized feedback through assignments is a cornerstone of education that supports their learning and development. Studie [...]
23 July 14:20-14:40 (add to calendar)	01A	Zahra Zare Jousheghani	Oarfish: Enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	HiTSeq: High Throughput Sequencing Algorithms & Applications	Motivation: Long read sequencing technology is becoming an increasingly indispensable tool in genomic and transcriptomic analysis. In transcriptomics [...]
23 July 14:20-14:40 (add to calendar)	01B	Chad Myers	Cytoscape Visualization Competition Results	NetBio: Network Biology
23 July 14:20-14:40 (add to calendar)	11BC	Laura Rumpf	Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data	RegSys: Regulatory and Systems Genomics	To gain insights into phenotype-specific gene regulation, we present our integrative analysis approach MetaFR harnessing single-cell epigenetic and tr [...]
23 July 14:20-14:40 (add to calendar)	02N	Xanthi Lida Katopodi	Charting the dynamics of the tRNAome in health and disease with AMaNITA	iRNA: Integrative RNA Biology	Transfer RNAs (tRNAs) play a pivotal role in decoding genetic information, determining which transcripts are highly and poorly translated at a given m [...]
23 July 14:40-15:00 (add to calendar)	03A	Charlotte Tumescheit	Ontology pre-training improves machine learning predictions of aqueous solubility and other metabolite properties	BOKR: Bio-Ontologies and Knowledge Representation	Predicting properties of small molecule metabolites from structures is a challenging task. Molecular language models have emerged as a highly performa [...]
23 July 14:40-15:00 (add to calendar)	01C	Alper Yurtseven	The Antimicrobial Resistance Prediction Challenge	CAMDA: Critical Assessment of Massive Data Analysis	Antimicrobial Resistance (AMR) is an urgent threat to human health worldwide as microbes have developed resistance to even the most advanced drugs. In [...]
23 July 14:40-15:00 (add to calendar)	12	Philip Blood	Flexible Hybrid Cloud Infrastructure Enabling Innovative Use and Long-Term Sustainability of Biomolecular Data and Reference Maps in HuBMAP and SenNet	ELIXIR/NIH-ODSS	We have established two successful NIH Common Fund Data Ecosystem (CFDE) data repositories and coordinating centers supporting the Human BioMolecular [...]
23 July 14:40-15:00 (add to calendar)	11A	Aparna Nathan	Teaching LLM literacy improves AI-aided data analysis in a bioinformatics course	Education: Computational Biology and Bioinformatics Education and Training	Large Language Model (LLM) tools (e.g., ChatGPT) are increasingly helping bioinformatics courses foster self-efficacy, personalize learning, and make [...]
23 July 14:40-15:00 (add to calendar)	01A	Leonardo Morelli	Identification of interactions defining 3D chromatin folding from micro to meso-scale	HiTSeq: High Throughput Sequencing Algorithms & Applications	Understanding the structural principles of chromatin organization is a central challenge in computational epigenomics, largely due to the sparse, nois [...]
23 July 14:40-15:20 (add to calendar)	01B	Fiona Brinkman	Microbiome multitudes and metadata madness	MICROBIOME	Microbiome analysis is increasingly becoming a critical component of a wide range of health, agri-foods, and environmental studies. I will present cas [...]
23 July 14:40-15:20 (add to calendar)	01B	Fiona Brinkman	Microbiome multitudes and metadata madness	NetBio: Network Biology	Microbiome analysis is increasingly becoming a critical component of a wide range of health, agri-foods, and environmental studies. I will present cas [...]
23 July 14:40-15:00 (add to calendar)	11BC	Vitalii Kleshchevnikov	Biophysical deep learning resolves how TF and DNA sequence specify the genome state of every cell population in human embryogenesis	RegSys: Regulatory and Systems Genomics	Understanding how interactions between transcription factors (TFs) and DNA sequence are orchestrated and give rise to the vast complexity of cell type [...]
23 July 14:40-15:00 (add to calendar)	02N	Lina Ma	Identification and characterization of chromatin-associated long non-coding RNAs in human	iRNA: Integrative RNA Biology	Chromatin-associated long non-coding RNAs (ca-lncRNAs) play crucial regulatory roles within the nucleus by preferentially binding to chromatin. Despit [...]
23 July 15:00-15:20 (add to calendar)	03A	Hande McGinty	Building the Aging Biomarkers Ontology and Its Applications in Aging Research	BOKR: Bio-Ontologies and Knowledge Representation	Aging is a complex biological process shaped by numerous biomarkers—such as cholesterol and blood sugar levels—that serve as measurable indicators of [...]
23 July 15:00-15:20 (add to calendar)	04AB	Kübra Narcı	Benchmarking Variant-Calling Workflows: The nf-core/variantbenchmarking Pipeline within the GHGA Framework	BioInfo-Core	The nf-core/variantbenchmarking pipeline (https://github.com/nf-core/variantbenchmarking) is a versatile and comprehensive workflow designed to benchm [...]
23 July 15:00-15:20 (add to calendar)	04AB	Thomas Roder	Assembly Curator: rapid and interactive consensus assembly generation for bacterial genomes	BioInfo-Core	Introduction Long-read sequencing technologies enable the generation of near-complete bacterial genome assemblies. However, no de novo assembler is pe [...]
23 July 15:00-15:20 (add to calendar)	01C	Owen Visser	Antimicrobial Resistance Prediction via Binary Ensemble Classifier and Assessment of Variable Importance	CAMDA: Critical Assessment of Massive Data Analysis	Antimicrobial resistance (AMR) presents a growing challenge to global health, driven by antibiotic overuse and the rapid evolution of resistant bacter [...]
23 July 15:00-15:20 (add to calendar)	01C	David Danko	A Highly Accurate Workflow for Inference of Antimicrobial Resistance from Genetic Data Based on Machine Learning and Global Data Curation	CAMDA: Critical Assessment of Massive Data Analysis	Note: This abstract is paired with the prediction submission “Base Model, 2nd Submission (Biotia)” made by user gfidler from team Biotia on May 15, 20 [...]
23 July 15:00-15:20 (add to calendar)	12	Martin Beracochea	Production workflows and orchestration at MGnify, ELIXIR’s Core Data Resource for metagenomics	ELIXIR/NIH-ODSS	MGnify is a key resource for the assembly, analysis and archiving of microbiome-derived sequencing datasets. Designed to be interoperable with the Eur [...]
23 July 15:00-15:20 (add to calendar)	11A	Inimary Toby-Ogundeji	Integrating Bioinformatics into Undergraduate Biology Education: Innovation, Experiential Learning, and Sustainable Program Design	Education: Computational Biology and Bioinformatics Education and Training	As biology becomes increasingly data-driven, the integration of computational and quantitative skills into undergraduate life sciences education is es [...]
23 July 15:00-15:20 (add to calendar)	01A	Liliana Florea	SpliSync: Genomic language model-driven splice site correction of long RNA reads	HiTSeq: High Throughput Sequencing Algorithms & Applications	We developed SpliSync, a deep learning method for accurate splice site correction in long read alignments. It combines a genomic language model, Hyena [...]
23 July 15:00-15:20 (add to calendar)	11BC	Surag Nair	Nona: A unifying multimodal masked modeling framework for functional genomics	RegSys: Regulatory and Systems Genomics	We present Nona, a unifying multimodal masked modeling paradigm for functional genomics. Nona is a neural network model that operates on both DNA sequ [...]
23 July 15:00-15:10 (add to calendar)	02N	Laura Veschetti	Toward a Computational Pipeline for Prokaryotic miRNAs: The Case of Pseudomonas aeruginosa in Lung Disease	iRNA: Integrative RNA Biology	Background: miRNAs are key regulators in eukaryotes, yet little is known about their existence and function in bacteria. Although various noncoding RN [...]
23 July 15:10-15:20 (add to calendar)	02N	Sofia Kudasheva	Characterisation of the role of SNORD116 in RNA processing during cardiomyocyte differentiation	iRNA: Integrative RNA Biology	Deletions of the SNORD116 small nucleolar RNA cluster result in Prader-Willi syndrome (PWS), a developmental disorder with a complex multisystem pheno [...]
23 July 15:20-15:40 (add to calendar)	03A	Richard Scheuermann	Discovering cellular contributions to disease pathogenesis in the NLM Cell Knowledge Network	BOKR: Bio-Ontologies and Knowledge Representation	Knowledge about the role of genes in disease pathogenesis has been obtained from genetic and genome-wide association studies. The proteins encoded by [...]
23 July 15:20-15:40 (add to calendar)	04AB	Adam Giess	Long Read Sequencing at Genomics England	BioInfo-Core	At Genomics England, in the Scientific R&D Team, we are evaluating the potential role of ‘long read’ technologies in clinical whole genome sequencing. [...]
23 July 15:20-15:40 (add to calendar)	04AB	Anil S. Thanki	Autonomous Single Cell Transcriptomics Analysis in Persist-seq	BioInfo-Core	The analysis of large-scale biological datasets poses considerable challenges, particularly in managing data complexity, ensuring reproducibility, and [...]
23 July 15:20-15:40 (add to calendar)	01C	Kinga Zielińska	The Gut Microbiome Health Index Challenge - Introduction	CAMDA: Critical Assessment of Massive Data Analysis
23 July 15:20-15:40 (add to calendar)	12	Robert Schuler	A SCALE-Able Approach to Building “Hybrid” Repositories to Drive Sustainable, Data Ecosystems	ELIXIR/NIH-ODSS	Scientific discovery increasingly relies on the ability to acquire, curate, integrate, analyze, and share vast and varied datasets. For instance, adva [...]
23 July 15:20-15:40 (add to calendar)	11A	Amanda Saravia-Butler	GeneLab for Colleges and Universities (GL4U): On-Demand Bioinformatics Training Using Space Biology Omics Data	Education: Computational Biology and Bioinformatics Education and Training	The NASA GeneLab project provides open access to space-relevant multi-omics data, hosted on the Open Science Data Repository (OSDR), which can be mine [...]
23 July 15:20-15:30 (add to calendar)	01A	Ghislain Fievet	adverSCarial: a toolkit for exposing classifier vulnerabilities in single-cell transcriptomics	HiTSeq: High Throughput Sequencing Algorithms & Applications	Adversarial attacks pose a significant risk to machine learning (ML) tools designed for classifying single-cell RNA-sequencing (scRNA-seq) data, with [...]
23 July 15:20-15:30 (add to calendar)	01B	Marija Dmitrijeva	Species-level taxonomic profiling of Earth’s microbiomes with mOTUs4	MICROBIOME	Microbial communities are crucial to the health and functioning of diverse ecosystems on Earth. A key step in their analysis is taxonomic profiling, i [...]
23 July 15:20-15:40 (add to calendar)	11BC	Tatevik Jalatyan	SCRIMPy: Single Cell Replication Inference from Multiome data using Python	RegSys: Regulatory and Systems Genomics	The cell cycle is a fundamental biological process crucial for an organism’s growth and development. Dysregulation of the cell cycle can lead to disea [...]
23 July 15:20-15:30 (add to calendar)	02N	Yaron Orenstein	EpiCRISPR: Improving CRISPR/Cas9 on-target efficiency prediction by multiple epigenetic marks, high-throughput datasets, and flanking sequences	iRNA: Integrative RNA Biology	CRISPR/Cas9 has transformed gene editing, enabling targeted modification of genomic loci using a 20-nt guide RNA followed by an NGG motif. However, ed [...]
23 July 15:30-15:40 (add to calendar)	01A	Netanya Keil	Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads	HiTSeq: High Throughput Sequencing Algorithms & Applications	SQANTI-reads leverages SQANTI3, a tool for the analysis of the quality of transcript models, to develop a read-level quality control framework for rep [...]
23 July 15:30-15:40 (add to calendar)	01B	Amine Ghozlane	Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2	MICROBIOME	The characterization of complex microbial communities is a critical challenge in microbiome research. Metagenomic profiling has advanced to include ta [...]
23 July 15:30-15:40 (add to calendar)	02N	Stefano Roncelli	Enhancing CRISPR/Cas9 Guide RNA Design Using Active Learning Techniques	iRNA: Integrative RNA Biology	CRISPR/Cas systems have significantly advanced genome editing, yet the precise design of guide RNAs (gRNAs) for optimal efficiency and specificity rem [...]
23 July 15:40-16:00 (add to calendar)	03A	Daniel Puthawala	Cat-VRS for Genomic Knowledge Curation: A Hyperintensional Representation Framework for FAIR Categorical Variation	BOKR: Bio-Ontologies and Knowledge Representation	Cat-VRS: A FAIR catvar Standard Categorical variants (catvars)—such as “MET exon 14 skipping” and “TP53 loss”—are foundational to genomic knowledge, l [...]
23 July 15:40-16:00 (add to calendar)	04AB	Iris Diana Yu	Advancing The Expression Atlas Resources: A Scalable Single-Cell Transcriptomics Pipeline to Facilitate Scientific Discoveries	BioInfo-Core	The Expression Atlas (https://www.ebi.ac.uk/gxa) and Single Cell Expression Atlas (https://www.ebi.ac.uk/gxa/sc) are EMBL-EBI knowledgebases for gene [...]
23 July 15:40-16:00 (add to calendar)	04AB	Ayushi Agrawal	Mixed effects models applied to single nucleus RNA-seq data identify cell types associated with animal level pathological trait of Alzheimer’s disease	BioInfo-Core	Apolipoprotein E4 (APOE4) is the strongest genetic risk factor for Alzheimer’s disease (AD). Although neuronal APOE4 expression is induced under condi [...]
23 July 15:40-16:00 (add to calendar)	04AB	Natalie Gill	Optimizing Clustering Resolution for Multi-subject Single Cell Studies	BioInfo-Core	Increasingly, single cell -omics analysis is being done on large cohorts of patients and model organisms and modularity based graph clustering algorit [...]
23 July 15:40-16:00 (add to calendar)	01C	Rafael Pérez Estrada	Integrating Taxonomic and Functional Features for Gut Microbiome Health Indexing	CAMDA: Critical Assessment of Massive Data Analysis	Accurate characterization of the gut microbiome is essential for understanding its role in health and disease; however, while current indices such as [...]
23 July 15:40-15:50 (add to calendar)	12	Fabio Liberante	From Platforms to Practice: How the ELIXIR Model Enables Impactful, Sustainable Biodata Resources	ELIXIR/NIH-ODSS	Biodata resources are only as impactful as the ecosystems in which they operate. ELIXIR provides a coordinated European infrastructure that supports t [...]
23 July 15:40-16:00 (add to calendar)	11A	Nadiia Kasianchuk	A Scalable Curriculum Model to Empower Rural Youth in Open Science Through Secondary Research and Peer-to-Peer Collaboration	Education: Computational Biology and Bioinformatics Education and Training	The Reuse Science School is a scalable, peer-oriented educational program designed to empower youth from rural and displaced communities in Ukraine th [...]
23 July 15:40-16:00 (add to calendar)	01A	Qian Shi	Transcriptome Assembly at Single-Cell Resolution with Beaver	HiTSeq: High Throughput Sequencing Algorithms & Applications	Motivation: The established single-cell RNA sequencing technologies (scRNA-seq) has revolutionized biological and biomedical research by enabling the [...]
23 July 15:40-15:50 (add to calendar)	01B	Shanfeng Zhu	Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes	MICROBIOME	Metagenomic binning is a culture-free approach that facilitates the recovery of metagenome-assembled genomes by grouping genomic fragments. However, t [...]
23 July 15:40-16:00 (add to calendar)	11BC	Jishnu Das	Uncovering Novel Cellular Programs and Regulatory Circuits Underlying Bifurcating Human B Cell States	RegSys: Regulatory and Systems Genomics	B cells upon antigen encounter undergo activation followed by a bifurcation either into extrafollicular plasmablasts (PB) or into germinal center (GC) [...]
23 July 15:40-16:00 (add to calendar)	02N	Syed Faraz Ahmed	Single-base tiled screen reveals design principles of PspCas13b-RNA targeting and informs automated screening of potent targets	iRNA: Integrative RNA Biology	The advancement of RNA therapeutics hinges on developing precise RNA-editing tools with high specificity and minimal off-target effects. We present a [...]
23 July 15:50-16:00 (add to calendar)	12	Ishwar Chandramouliswaran	NIH-ODSS Data Repository Landscape	ELIXIR/NIH-ODSS	This talk will share about the NIH data repository landscape and associated program initiatives [...]
23 July 15:50-16:00 (add to calendar)	01B	Nils Kleinbölting	Metagenomics-Toolkit: The Flexible and Efficient Cloud-Based Metagenomics Workflow	MICROBIOME	The metagenome analysis of complex environments with thousands of datasets, such as those available in the Sequence Read Archive, requires immense com [...]
23 July 16:40-17:40 (add to calendar)	03A	Ian Horrocks	Knowledge Graphs: Theory, Applications and Challenges	BOKR: Bio-Ontologies and Knowledge Representation	Knowledge Graphs have rapidly become a mainstream technology that combines features of databases and AI. In this talk I will introduce Knowledge Graph [...]
23 July 16:40-17:00 (add to calendar)	04AB	Hubert Rehrauer	GEO Uploader: Simplifying the data deposition in the GEO repository	BioInfo-Core	Introduction Making data FAIR is a key step in every research project. For NGS data there are the GEO and ENA repositories that provide long term stor [...]
23 July 16:40-17:00 (add to calendar)	04AB	Carlos Prieto	Enhancing Bioinformatics Workflows with Analytical Visualization Tools	BioInfo-Core	Current front end development technologies have enabled the development of new visual analytics tools. These methodologies allow data to be visualized [...]
23 July 16:40-17:00 (add to calendar)	04AB	Patricia Carvajal-López	Competency framework profiles to reflect career progression within bioinformatics core facility scientists	BioInfo-Core	There is an expanding need for specialised services from Bioinformatics Core Facilities (BCF). Providing services for these infrastructures requires h [...]
23 July 16:40-17:20 (add to calendar)	01C		Building a Rare-Disease Microbiome Health Index: Integrating Gut Metagenomes, Synthetic PKU EHRs and Rare-Variant Profiles to Forecast Phenylalanine Crises	CAMDA: Critical Assessment of Massive Data Analysis	Phenylketonuria (PKU) is an autosomal recessive metabolic disorder characterized by deficient phenylalanine hydroxylase activity, leading to episodic [...]
23 July 16:40-18:00 (add to calendar)	02F		CollaborationFest	CollaborationFest
23 July 16:40-17:00 (add to calendar)	12	Melissa Harrison	Meeting user expectations in a resource constrained environment: Europe PMC’s approach	ELIXIR/NIH-ODSS	Artificial intelligence (AI), in particular generative AI, is rapidly changing the expectations of researchers and how they approach literature search [...]
23 July 16:40-17:00 (add to calendar)	11A	Nicola Mulder	Capacity Building for Pathogen Surveillance through Pathogen Genomics and Bioinformatics Training in Africa	Education: Computational Biology and Bioinformatics Education and Training	The recent emergence and re-emergence of infectious diseases in Africa highlight the critical need for robust pathogen genomic surveillance systems ac [...]
23 July 16:40-17:00 (add to calendar)	01A	Elizabeth Tseng	Bioinformatics analysis for long-read RNA sequencing: challenges and promises	HiTSeq: High Throughput Sequencing Algorithms & Applications	Long-read RNA sequencing has emerged as a powerful tool in transcriptomics, offering the ability to sequence full-length cDNAs—often exceeding 10 kb—w [...]
23 July 16:40-17:20 (add to calendar)	01B		TBA	MICROBIOME
23 July 16:40-17:00 (add to calendar)	11BC	Jacob Schreiber	Ledidi: Programmatic design and editing of cis-regulatory elements	RegSys: Regulatory and Systems Genomics	The development of modern genome editing tools has enabled researchers to make such edits with high precision, but has left unsolved the problem of de [...]
23 July 16:40-17:20 (add to calendar)	02N	Roser Vento-Tormo	Gene regulation of human cell systems	iRNA: Integrative RNA Biology	The study of human tissues requires a systems biology approach. Their development starts in utero and during adulthood, they change their organization [...]
23 July 17:00-18:00 (add to calendar)	04AB		Breakout Groups	BioInfo-Core	Our unconferencing event - attendees will break into groups based on topics of interest to discuss further with other core members. [...]
23 July 17:00-17:20 (add to calendar)	12	Mark Hahnel	Coopetition as a Catalyst for Researcher Engagement with Open Data	ELIXIR/NIH-ODSS	The NIH GREI (Generalist Repository Ecosystem Initiative) aims to enhance data sharing and reuse of NIH-funded research by fostering collaboration amo [...]
23 July 17:00-17:20 (add to calendar)	11A	Alina Frolova	The emerging ecosystem of competitive educational programs in bioinformatics in Ukraine	Education: Computational Biology and Bioinformatics Education and Training	Competitive education in the areas of bioinformatics, computational biology, and biological data analysis has become a pass to the world of modern bio [...]
23 July 17:00-18:00 (add to calendar)	01A	Jonathan Göke	Quantifying RNA Expression and Modifications using Long Read RNA-Seq	HiTSeq: High Throughput Sequencing Algorithms & Applications	The human genome contains instructions to transcribe more than 200,000 RNAs. However, many RNA transcripts are generated from the same gene, resulting [...]
23 July 17:00-17:20 (add to calendar)	11BC	Laura Gunsalus	Lilliput: Compact native regulatory element design with machine learning-guided miniaturization	RegSys: Regulatory and Systems Genomics	Size-limited gene therapy vectors require compact cell type-specific regulatory elements. Existing miniaturized sequences have been hand-selected and [...]
23 July 17:20-17:40 (add to calendar)	01C	Vincent Mei	Toward the Development of a Novel and Comprehensive Gut Health Index: An Ensemble Model Integrating Taxonomic and Functional Profiles	CAMDA: Critical Assessment of Massive Data Analysis	Diseases linked to the gut microbiome have been on the rise, which contributes to the rising cost of healthcare and worsening patient outcomes . Since [...]
23 July 17:20-17:40 (add to calendar)	12	Eleni Tzampatzopoulou	Evaluating the Impact of Biodata Resources: Insights from EMBL-EBI’s Impact Assessments	ELIXIR/NIH-ODSS	The provision of open access data through biodata resources is a critical driver of breakthroughs in life sciences research, advances in clinical prac [...]
23 July 17:20-18:00 (add to calendar)	11A	Patricia Carvajal-López	Fostering communities of practice in bioinformatics education and training	Education: Computational Biology and Bioinformatics Education and Training	Communities of practice in bioinformatics education and training are essential, both for the technical training and professional development of bioinf [...]
23 July 17:20-17:40 (add to calendar)	01B	Weimin Wu	DNABERT-S: Pioneering Species Differentiation with Species-Aware DNA Embeddings	MICROBIOME	We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different s [...]
23 July 17:20-18:00 (add to calendar)	11BC	Mafalda Dias	What can the diversity of life of Earth teach us about disease?	RegSys: Regulatory and Systems Genomics	Biological sequences across the tree of life reflect the cumulative effects of millions of years of evolution. Modelling variation in these sequences [...]
23 July 17:20-17:40 (add to calendar)	02N	Jacob Munro	EdiSetFlow: A robust pipeline for RNA editing detection and differential analysis in bulk RNA-seq	iRNA: Integrative RNA Biology	Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional modification catalyzed by ADAR enzymes that can alter codons, splicing patterns, a [...]
23 July 17:40-17:45 (add to calendar)	03A	Mark Streer	Bridging Language Barriers in Bio-Curation: An LLM-Enhanced Workflow for Ontology Translation into Japanese	BOKR: Bio-Ontologies and Knowledge Representation	SciBite’s ontology management and named entity recognition (NER) software relies on curated public ontologies to support data harmonization under FAIR [...]
23 July 17:40-18:00 (add to calendar)	01C	Doroteya Staykova	Topology-Enabled Integration of Taxonomic and Functional Microbiome Profiles Reveals Distinct Subgroups in Healthy Individuals	CAMDA: Critical Assessment of Massive Data Analysis	High-throughput sequencing technologies have enabled detailed taxonomic and functional profiling of the human gut microbiome. However, integrating the [...]
23 July 17:40-18:00 (add to calendar)	01C		Ensemble-Based Topic Selection for Text Classification via a Grouping, Scoring, and Modeling Approach	CAMDA: Critical Assessment of Massive Data Analysis	The exponential growth in scientific literature, especially in biomedical domains, has intensified the need for effective automatic text classificatio [...]
23 July 17:40-18:00 (add to calendar)	12	Alex Bateman	Beyond Citations: Measuring the Economic and Scientific Impact of UniProt in the Biodata Ecosystem	ELIXIR/NIH-ODSS	This talk presents a comprehensive cost-benefit analysis of UniProt, the universal protein resource that serves as a crucial catalogue for protein dat [...]
23 July 17:40-17:50 (add to calendar)	01B	Tatiana Gurbich	MGnify Genomes: generating richly annotated, searchable biome-specific genome catalogues	MICROBIOME	The generation of metagenome-assembled genomes (MAGs) has become a routine method for studying microbiomes. With the growing availability of MAGs in p [...]
23 July 17:40-18:00 (add to calendar)	02N	Liang Huang	EnsembleDesign: Messenger RNA Design Minimizing Ensemble Free Energy via Probabilistic Lattice Parsing	iRNA: Integrative RNA Biology	The task of designing optimized messenger RNA (mRNA) sequences has received much attention in recent years thanks to breakthroughs in mRNA vaccines du [...]
23 July 17:45-17:50 (add to calendar)	03A	Felix Shaw	Enabling FAIR Single-Cell RNAseq Data Management with COPO	BOKR: Bio-Ontologies and Knowledge Representation	We present our work on establishing standards and tools for validating and submitting single-cell RNA sequencing (scRNA-seq) data and metadata using t [...]
23 July 17:50-17:55 (add to calendar)	03A	Susheel Varma	Cancer Complexity Knowledge Portal: A centralized web portal for finding cancer related data, software tools, and other resources	BOKR: Bio-Ontologies and Knowledge Representation	Applying artificial intelligence and machine learning to biomedical problems requires clean, high-quality data and reusable software tools. The Cancer [...]
23 July 17:50-18:00 (add to calendar)	01B	Johanna von Wachsmann	Rapid and Consistent Genome Clustering for Navigating Bacterial Diversity with Millions of Genomes	MICROBIOME	The exponential growth of bacterial genomic databases presents unprecedented challenges for researchers, with isolate genomes increasing from 661,405 [...]
23 July 17:55-18:00 (add to calendar)	03A		COSI Closing Remarks	BOKR: Bio-Ontologies and Knowledge Representation
23 July 18:00-18:45 (add to calendar)	-		JPI Meet-Up	Special Track
24 July 08:40-08:45 (add to calendar)	04AB		Opening	BioVis: Biological Data Visualizations
24 July 08:40-09:40 (add to calendar)	01C	Spiros Denaxas	Data, Diagnoses, and Discovery: Improving Healthcare through Electronic Health Records	CAMDA: Critical Assessment of Massive Data Analysis	Electronic health records (EHRs) represent rich, multidimensional data generated through routine interactions within the healthcare system. These reco [...]
24 July 08:40-10:00 (add to calendar)	02F		CollaborationFest	CollaborationFest
24 July 08:40-09:00 (add to calendar)	03A	Dongmin Bang	ADME-Drug-Likeness: Enriching Molecular Foundation Models via Pharmacokinetics-Guided Multi-Task Learning for Drug-likeness Prediction	GenCompBio: General Computational Biology	Recent breakthroughs in AI-driven generative models enable the rapid design of extensive molecular libraries, creating an urgent need for fast and acc [...]
24 July 08:40-09:40 (add to calendar)	01A	Tobias Marschall	Pangenome based analysis of structural variation	HiTSeq: High Throughput Sequencing Algorithms & Applications	Breakthroughs in long-read sequencing technology and assembly methodology enable the routine de novo assembly of human genomes to near completion. Suc [...]
24 July 08:40-09:00 (add to calendar)	01B	Jiayu Shang	GiantHunter: Accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search	MICROBIOME	Motivation: Nucleocytoplasmic large DNA viruses (NCLDVs) are notable for their large genomes and extensive gene repertoires, which contribute to their [...]
24 July 08:40-09:20 (add to calendar)	11BC	Roser Vento-Tormo	“Gene regulation of human cell systems”	RegSys: Regulatory and Systems Genomics	“The study of human tissues requires a systems biology approach. Their development starts in utero and during adulthood, they change their organizatio [...]
24 July 08:40-09:00 (add to calendar)	03B		Introduction	Stewardship Critical Infrastructure
24 July 08:40-09:00 (add to calendar)	12		Opening remarks	Text Mining: Text Mining for Healthcare and Biology
24 July 08:40-09:00 (add to calendar)	02N	Christina Kalk	Prediction and validation of Split Open Reading Frames across cell types	iRNA: Integrative RNA Biology	Background: Split Open Reading frames (Split-ORFs) exist on transcripts containing at least two open reading frames, each of which encodes a part of t [...]
24 July 08:45-09:40 (add to calendar)	04AB	Kay Nieselt	The Visual Genome: An attempt to classify multi-omics visualization	BioVis: Biological Data Visualizations	Over the past decades, advances in biology and medicine—driven by high-throughput and high-resolution experimental methods—have underscored the critic [...]
24 July 09:00-09:20 (add to calendar)	03A	Nikhil Branson	Understanding the Sources of Performance in Deep Drug Response Models Reveals Insights and Improvements	GenCompBio: General Computational Biology	Anti-cancer drug response prediction (DRP) using cancer cell lines (CLs) is crucial in stratified medicine and drug discovery. Recently new deep learn [...]
24 July 09:00-09:10 (add to calendar)	01B	Fernando Meyer	CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software	MICROBIOME	Finding appropriate software and parameter settings to process shotgun metagenome data is essential for meaningful metagenomic analyses. To enable obj [...]
24 July 09:00-09:20 (add to calendar)	03B	Alex Bateman	Beyond Citations: Measuring the Economic and Scientific Impact of UniProt in the Biodata Ecosystem	Stewardship Critical Infrastructure	This talk presents a comprehensive cost-benefit analysis of UniProt, the universal protein resource that serves as a crucial catalogue for protein dat [...]
24 July 09:00-09:40 (add to calendar)	12		Keynote - TBA	Text Mining: Text Mining for Healthcare and Biology
24 July 09:00-09:20 (add to calendar)	02N	Ilyes Baali	Bridging the Gap: Recalibrating In-vitro Models for Accurate In-vivo RBP Binding Predictions	iRNA: Integrative RNA Biology	Accurate identification of RNA-binding protein (RBP) binding sites is essential for understanding post-transcriptional gene regulation. However, curre [...]
24 July 09:10-09:20 (add to calendar)	01B	Alice McHardy	CAMI community exchange	MICROBIOME
24 July 09:20-09:40 (add to calendar)	03A	Gwang-Hyeon Yun	FACT: Feature Aggregation and Convolution with Transformers for predicting drug classification code	GenCompBio: General Computational Biology	Motivation: Drug repositioning, identifying new therapeutic applications for existing drugs, can significantly reduce the time and cost involved in dr [...]
24 July 09:20-09:30 (add to calendar)	01B	Wenhuan Zeng	NanoGraph: Mapping Nanopore Squiggles to Graphs Enables Accurate Taxonomic Assignment	MICROBIOME	Nanopore sequencing technology offers long sequencing reads and real-time analysis capabilities, making it a powerful tool for addressing diverse ques [...]
24 July 09:20-09:40 (add to calendar)	11BC	Gary Hu	Anomaly Detection in Spatial Transcriptomics via Spatially Localized Density Comparison	RegSys: Regulatory and Systems Genomics	Motivation Perturbations in biological tissues – e.g. due to inflammation, disease, or drug treatment – alter the composition of cell types and cell s [...]
24 July 09:20-09:40 (add to calendar)	03B	Shoba Ranganathan	Challenges in biological data/infrastructure stewardship from an Asia-Pacific perspective	Stewardship Critical Infrastructure	The Asia-Pacific (APAC) region covers countries and territories in Australasia, East Asia, and Southeast Asia are often included. In a wider context, [...]
24 July 09:20-09:40 (add to calendar)	02N	Adi Gershon	Multi-Tool Intron Retention Analysis in Autism	iRNA: Integrative RNA Biology	Intron retention is an alternative splicing event in which introns remain in mature mRNA, altering protein isoforms or triggering transcript decay. Re [...]
24 July 09:30-09:40 (add to calendar)	01B	Anupam Gautam	MEGAN7: Enhanced Optimization and Advanced Functionality for Metagenomic Analysis	MICROBIOME	MEGAN is a widely used, user-friendly tool for metagenomic analysis, suitable for long and short read data, and remains the only tool with a GUI inter [...]
24 July 09:40-10:00 (add to calendar)	04AB	Bum Chul Kwon	GENET: AI-Powered Interactive Visualization Workflows to Explore Biomedical Entity Networks	BioVis: Biological Data Visualizations	Formulating experimental hypotheses that test the association between SNPs and diseases involves logical reasoning derived from prior observations, fo [...]
24 July 09:40-10:00 (add to calendar)	01C	Daniel Voskergian	Stage-Disease Grouping, Scoring, and Modeling for Predicting Diabetes Complications from Electronic Health Records	CAMDA: Critical Assessment of Massive Data Analysis	Diabetes mellitus remains a major global health challenge, contributing significantly to morbidity, disability, and mortality. Accurate prediction of [...]
24 July 09:40-10:00 (add to calendar)	03A	Ankit	Efficient 3D kernels for molecular property prediction	GenCompBio: General Computational Biology	This paper addresses the challenge of incorporating 3-dimensional structural information in graph kernels for machine learning-based virtual screening [...]
24 July 09:40-10:00 (add to calendar)	01A	Mike Vella	Latest advances in bioinformatics for Oxford Nanopore data	HiTSeq: High Throughput Sequencing Algorithms & Applications	Oxford Nanopore Technologies has transformed genomics with real-time, long-read sequencing capable of detecting epigenetic modifications and structura [...]
24 July 09:40-09:50 (add to calendar)	01B	Feargal Ryan	TaxSEA: Rapid Interpretation of Microbiome Alterations Using Taxon Set Enrichment Analysis and Public Databases	MICROBIOME	Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most current to [...]
24 July 09:40-10:00 (add to calendar)	11BC		Flash Talk Session 2	RegSys: Regulatory and Systems Genomics	Session with 4 short talks: Maxime Christophe - Interpretable deep learning reveals sequence determinants of nucleosome positioning in mammalian genom [...]
24 July 09:40-10:00 (add to calendar)	03B	Deepak Nair	Indian Biological Data Centre: past, present and future	Stewardship Critical Infrastructure	The Indian Biological Data Centre (IBDC) is the first digital repository mandated to archive and share all biological data generated in India. The IBD [...]
24 July 09:40-10:00 (add to calendar)	12		Poster lightning talks	Text Mining: Text Mining for Healthcare and Biology
24 July 09:40-10:00 (add to calendar)	02N	Timothy Warwick	Detection of statistically robust interactions from diverse RNA-DNA ligation data	iRNA: Integrative RNA Biology	Background: Chromatin-localized RNAs play key roles in gene regulation and nuclear architecture. Genome-wide RNA-DNA interactions can be mapped using [...]
24 July 09:50-10:00 (add to calendar)	01B	Junhua Li	SinProVirP: a Signature Protein-based Approach for Accurate and Efficient Profiling of the Human Gut Virome	MICROBIOME	The human gut virome represents a critical yet underexplored microbial component that regulates bacterial communities, modulates host immunity, and ma [...]
24 July 11:20-11:40 (add to calendar)	04AB	Olaitan I. Awe	Prostruc: an open-source tool for 3D structure prediction using homology modeling	BioVis: Biological Data Visualizations	Homology modeling is a widely used computational technique for predicting the three-dimensional (3D) structures of proteins based on known templates,e [...]
24 July 11:20-12:00 (add to calendar)	01C	Antti Honkela	Benchmarking for Better Private Algorithms	CAMDA: Critical Assessment of Massive Data Analysis	Responsible application of machine learning (ML) on sensitive health and genetic data requires privacy-preserving algorithms to ensure that the data a [...]
24 July 11:20-13:00 (add to calendar)	02F		CollaborationFest	CollaborationFest
24 July 11:20-11:40 (add to calendar)	03A	Tanveer Ahmad	Haplotype-specific copy number profiling of cancer genomes from long reads sequencing data	GenCompBio: General Computational Biology	Attached as PDF [...]
24 July 11:20-11:40 (add to calendar)	01A	Mikaël Salson	CREMSA: Compressed Indexing of (Ultra) Large Multiple Sequence Alignments	HiTSeq: High Throughput Sequencing Algorithms & Applications	Recent viral outbreaks motivate a systematic collection of pathogenic genomes, including a strong focus on genomic RNA, in order to accelerate their s [...]
24 July 11:20-11:40 (add to calendar)	01B	Conrad Testagrose	Leveraging Large Language Models to Predict Antibiotic Resistance in Mycobacterium tuberculosis	MICROBIOME	Antibiotic resistance in Mycobacterium tuberculosis (MTB) poses a significant challenge to global public health. Rapid and accurate prediction of anti [...]
24 July 11:20-11:40 (add to calendar)	11BC	Uthsav Chitra	GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts	RegSys: Regulatory and Systems Genomics	Motivation: Gene expression varies across a tissue due to both the organization of the tissue into spatial domains, i.e. discrete regions of a tissue [...]
24 July 11:20-11:40 (add to calendar)	03B	Julio Collado Vides	A Proposal on top of FAIR: Quality of Knowledge Representation (QKR)	Stewardship Critical Infrastructure	The FAIR (Findable, Accessible, Interoperable, and Reusable ) principles define the current standard for data representation. However, there is still [...]
24 July 11:20-11:40 (add to calendar)	12	Noam H. Rotenberg	Representations of Cells in the Biomedical Literature: First Look at the NLM CellLink Corpus	Text Mining: Text Mining for Healthcare and Biology	Single-cell technologies are enabling the discovery of many novel cell phenotypes, but this growing body of knowledge remains fragmented across the sc [...]
24 July 11:20-13:00 (add to calendar)	11A		Exchanging experience and use cases of working cross-sector	WEB: Workshop on Education for Bioinformatics	The panel will share and explore their experiences of organising and delivering across industry,clinical and academic sectors. Highlighting both the c [...]
24 July 11:20-11:50 (add to calendar)	02N	Blake Sweeney	Building the future of RNA tools	iRNA: Integrative RNA Biology	From the epitranscriptome and 3D structure prediction to large language models, RNA science is experiencing a transformative shift. Recent advances in [...]
24 July 11:40-12:00 (add to calendar)	04AB	Zeynep H. Gümüş	ClusterChirp: A GPU-Accelerated Web Platform for AI-Supported Interactive Exploration of High-Dimensional Omics Data	BioVis: Biological Data Visualizations	Modern omics technologies generate high-dimensional datasets that overwhelm traditional visualization tools, requiring computational tradeoffs that r [...]
24 July 11:40-12:00 (add to calendar)	03A	Pushpa Itagi	Multi-omics and liquid biopsy profiling of rapid autopsies reveals evolutionary dynamics and heterogeneity in metastatic bladder cancer	GenCompBio: General Computational Biology	The extensive molecular, transcriptomic and genomic complexity of metastatic bladder cancer (mBLCA) significantly complicates clinical management. App [...]
24 July 11:40-12:00 (add to calendar)	01A	Nicola Rizzo	Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs	HiTSeq: High Throughput Sequencing Algorithms & Applications	Sequence-to-graph alignment is a central challenge of computational pangenomics. To overcome the theoretical hardness of the problem, state-of-the-art [...]
24 July 11:40-11:50 (add to calendar)	01B	Johannes Soeding	De novo discovery of conserved gene clusters in microbial genomes with Spacedust	MICROBIOME	Metagenomics has revolutionized environmental and human-associated microbiome studies. However, the limited fraction of proteins with known biological [...]
24 July 11:40-12:00 (add to calendar)	11BC	Merle Stahl	Refinement Strategies for Tangram for Reliable Single-Cell to Spatial Mapping	RegSys: Regulatory and Systems Genomics	Motivation: Single-cell RNA sequencing (scRNA-seq) provides comprehensive gene expression data at a single-cell level but lacks spatial context. In co [...]
24 July 11:40-12:00 (add to calendar)	03B		Perspectives on biological knowledgebase management and the advent of AI	Stewardship Critical Infrastructure
24 July 11:40-12:00 (add to calendar)	12	Connor Grannis	Contextualizing phenotypes in medical notes with small language models	Text Mining: Text Mining for Healthcare and Biology	Accurate phenotypic extraction from clinical notes is essential for precision medicine. While manual approaches are time-consuming and prone to bias, [...]
24 July 11:50-12:00 (add to calendar)	01B	Ilia Olkhovskii	Nerpa 2: linking biosynthetic gene clusters to nonribosomal peptide structures	MICROBIOME	Nonribosomal peptides (NRPs) are clinically important molecules produced by microbial specialized enzymes encoded in biosynthetic gene clusters (BGCs) [...]
24 July 11:50-12:00 (add to calendar)	02N	Etienne Boileau	Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites promoting cross-disciplinary collaborative research	iRNA: Integrative RNA Biology	We recently presented Sci-ModoM [1], the first next-generation RNome database offering a one-stop source for RNA modifications originating from state- [...]
24 July 12:00-12:20 (add to calendar)	04AB	Qianwen Wang	Can LLMs Bridge Domain and Visualization? A Case Study onHigh-Dimension Data Visualization in Single-Cell Transcriptomics	BioVis: Biological Data Visualizations	While many visualizations are built for domain users (biologists), understanding how visualizations are used in the domain has long been a challenging [...]
24 July 12:00-12:20 (add to calendar)	01C	Hakime Öztürk	The Health Privacy Challenge - Introduction	CAMDA: Critical Assessment of Massive Data Analysis	The Health Privacy Challenge, which is organized in the context of the European Lighthouse on Safe and Secure AI (ELSA, https://elsa-ai.eu/), explores [...]
24 July 12:00-12:20 (add to calendar)	03A	Oscar González Velasco	Using spatial transcriptomics to elucidate the primary site of Cancers of Unknown Primary (CUPs)	GenCompBio: General Computational Biology	Cancers of unknown primary (CUP) are a challenging group of poorly differentiated metastatic cancers, that due to its nature limited treatment options [...]
24 July 12:00-12:20 (add to calendar)	01A	Ondřej Sladký	FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)	HiTSeq: High Throughput Sequencing Algorithms & Applications	The exponential growth of DNA sequencing data calls for efficient solutions for storing and querying large-scale k-mer sets. While recent indexing app [...]
24 July 12:00-12:10 (add to calendar)	01B	Xiaoquan Su	Phylo-Spec: a phylogeny-fusion deep learning model advances microbiome status identification	MICROBIOME	Motivation: The human microbiome is crucial for health regulation and disease progression, presenting a valuable opportunity for health state classifi [...]
24 July 12:00-12:20 (add to calendar)	11BC	Cassandra Burdziak	Encoding single-cell chromatin landscapes as probability distributions with optimal transport	RegSys: Regulatory and Systems Genomics	Single-cell measurement of paired epigenetic and transcriptomic features is becoming routine, and promises to license more sophisticated models of gen [...]
24 July 12:00-12:20 (add to calendar)	03B	Peter Maccallum	Developing stewardship networks to sustain data, software and systems	Stewardship Critical Infrastructure
24 July 12:00-12:20 (add to calendar)	12	Danilo Tomasoni	CSpace: A concept embedding space for bio-medical applications	Text Mining: Text Mining for Healthcare and Biology	Motivation: The rise of transformer-based architectures dramatically improved our ability to analyze natural language. However, the power and flexibil [...]
24 July 12:00-12:10 (add to calendar)	02N	A. Ercument Cicek	RNAtranslator: A Generative Language Model for Protein-Conditional RNA Design	iRNA: Integrative RNA Biology	Protein-RNA interactions are essential in gene regulation, splicing, RNA stability, and translation, making RNA a promising therapeutic agent for targ [...]
24 July 12:10-12:20 (add to calendar)	01B	Petra Matyskova	Beyond Taxonomy and Function: Protein Language Models for Scalable Microbial Representations	MICROBIOME	Traditional microbial representations based on taxonomy or functional annotations like KEGG Orthology (KOs) and OrthoFinder groups (OGs) suffer from l [...]
24 July 12:10-12:20 (add to calendar)	02N	Giulia Cantini	miRXplain: transformer-driven explainable microRNA target prediction leveraging isomiR interactions	iRNA: Integrative RNA Biology	microRNAs (miRNAs) are short (~22 nt) RNA sequences key regulators of transcript expression. miRNAs bind to target mRNA sites to repress genes. isomiR [...]
24 July 12:20-12:40 (add to calendar)	04AB	Thomas C. Smits	Automatic Generation of Natural Language Descriptions of Genomics Data Visualizations for Accessibility and Machine Learning	BioVis: Biological Data Visualizations	Availability of multimodal representations, i.e., visual and textual, is crucial for both information accessibility and construction of retrieval syst [...]
24 July 12:20-13:00 (add to calendar)	01C		The Health Privacy - panel discussion	CAMDA: Critical Assessment of Massive Data Analysis
24 July 12:20-12:40 (add to calendar)	03A	Zeynep H. Gümüş	Inherited genetic risk factors associated with young adult versus late-onset lung cancers	GenCompBio: General Computational Biology	Genetics plays a key role in lung cancer risk. While lung cancer primarily affects older adults, incidence among young adults is increasing. However [...]
24 July 12:20-12:40 (add to calendar)	01A	Roland Faure	The Alice assembler: dramatically accelerating genome assembly with MSR sketching	HiTSeq: High Throughput Sequencing Algorithms & Applications	The PacBio HiFi technology and the R10.4 Oxford Nanopore flowcells are transforming the genomic world by producing for the first time long and accurat [...]
24 July 12:20-12:30 (add to calendar)	01B	Ali Rahnavard	Guided tokenizer enhances metagenomic language models performance	MICROBIOME	Tokenization is a critical step in adapting language models for genomic and metagenomic sequence analysis. Traditional tokenization methods—such as fi [...]
24 July 12:20-12:40 (add to calendar)	11BC	Laura D. Martens	scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution	RegSys: Regulatory and Systems Genomics	Understanding how regulatory sequences shape gene expression across individual cells is a fundamental challenge in genomics. Joint RNA-seq and epigeno [...]
24 July 12:20-12:40 (add to calendar)	03B		Technical Discussion	Stewardship Critical Infrastructure
24 July 12:20-12:40 (add to calendar)	12	Rahul Brahma	VectorSage: Enhancing PubMed Article Retrieval with Advanced Semantic Search	Text Mining: Text Mining for Healthcare and Biology	The exponential growth of academic literature has presented unprecedented opportunities and highlighted the need for advanced search methodologies for [...]
24 July 12:20-12:30 (add to calendar)	02N	Cho Joohyun	Designing functional RNA sequences using conditional diffusion models	iRNA: Integrative RNA Biology	The function of RNA is largely determined by its networks of protein-RNA interactions. A key challenge in RNA engineering is in designing the sequence [...]
24 July 12:30-12:40 (add to calendar)	01B	Daniel Gómez-Pérez	REMAG: recovery of eukaryotic genomes from metagenomes using reference-free contrastive learning	MICROBIOME	Assembly-based metagenomic approaches, including generation of metagenome‑assembled genome (MAG) catalogues, are pivotal for exploring and understandi [...]
24 July 12:30-13:00 (add to calendar)	02N		The future of RNA tools	iRNA: Integrative RNA Biology
24 July 12:40-13:00 (add to calendar)	04AB	Daniel Huson	Sketch, capture and layout Phylogenies	BioVis: Biological Data Visualizations	Phylogenetic trees and networks play a central role in biology, bioinformatics, and mathematical biology, and producing clear, informative visualizati [...]
24 July 12:40-13:00 (add to calendar)	04AB	Maik Wolfram-Schauerte	PhageExpressionAtlas - a comprehensive transcriptional atlas of phage infections of bacteria	BioVis: Biological Data Visualizations	Bacteriophages (phages) are bacterial viruses that infect and lyse their hosts. Phages shape microbial ecosystems and have contributed essential tools [...]
24 July 12:40-13:00 (add to calendar)	03A	Carlos Angel	pC-SAC: Method for High-Resolution 3D Genome Reconstruction from Low-Resolution Hi-C Data	GenCompBio: General Computational Biology	The three-dimensional (3D) organization of the genome is crucial for gene regulation, with disruptions linked to various diseases. High-throughput Chr [...]
24 July 12:40-13:00 (add to calendar)	01A	Noam Teyssier	BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences	HiTSeq: High Throughput Sequencing Algorithms & Applications	Modern genomics routinely generates billions of sequencing records per run, typically stored as gzip-compressed FASTQ files. This format's inherent li [...]
24 July 12:40-12:50 (add to calendar)	01B	Tomas Vinar	Flexible Log-odds Homology Features for Plasmid Identification	MICROBIOME	We study the problem of plasmid identification in short-read assemblies of bacterial isolates. The goal is to classify individual contigs as coming fr [...]
24 July 12:40-13:00 (add to calendar)	11BC	Dante Bolzan	Soffritto: a deep-learning model for predicting high-resolution replication timing	RegSys: Regulatory and Systems Genomics	Motivation: Replication Timing (RT) refers to the order by which DNA loci are replicated during S phase. RT is cell-type specific and implicated in ce [...]
24 July 12:40-13:00 (add to calendar)	12	Melike Akkaya	Large Language Model Applications on the Uniprot Protein Sequence and Annotation Database	Text Mining: Text Mining for Healthcare and Biology	Efficiently accessing and analyzing comprehensive biological datasets remains challenging due to traditional querying complexities. To address this, w [...]
24 July 12:50-13:00 (add to calendar)	01B	Pau Piera Lindez	Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning	MICROBIOME	Plasmids are extrachromosomal DNA molecules that enable horizontal gene transfer in bacteria, often conferring advantages such as antibiotic resistanc [...]
24 July 14:00-14:40 (add to calendar)	04AB	Simon Warchol	SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data	BioVis: Biological Data Visualizations	Dimensionality reduction techniques help analysts interpret complex, high-dimensional spatial datasets by projecting data attributes into two-dimensio [...]
24 July 14:00-14:40 (add to calendar)	04AB	Swaathi Kandasaamy	Nightingale - A collection of web components for visualizing protein related data	BioVis: Biological Data Visualizations	Nightingale is an open-source web visualization library for rendering protein-related data including domains, sites, variants, structures, and interac [...]
24 July 14:00-14:40 (add to calendar)	04AB	Huyen N. Nguyen	A Multimodal Search and Authoring System for Genomics Data Visualizations	BioVis: Biological Data Visualizations	We present a database system for retrieving interactive genomics visualizations through multimodal search capabilities. Our system offers users flexib [...]
24 July 14:00-14:40 (add to calendar)	04AB	Tomasz Kurowski	Tersect Browser: characterising introgressions through interactive visualisation of large numbers of resequenced genomes	BioVis: Biological Data Visualizations	Introgressive hybridisation has long been a major source of genetic variation in plant genomes, and the ability to precisely identify and delimit inte [...]
24 July 14:00-14:20 (add to calendar)	01C	Andrew Wicks	Synthetic genomic data generation through Differential Privacy-enhanced Non-Negative Matrix Factorization (DP-NMF)	CAMDA: Critical Assessment of Massive Data Analysis	Generation of synthetic genomics data is increasingly considered as a routine approach for safely sharing sensitive genomic datasets. While traditiona [...]
24 July 14:00-16:00 (add to calendar)	02F		CollaborationFest	CollaborationFest
24 July 14:00-14:20 (add to calendar)	03A	Franziska Görtler	HIDE: Hierarchical cell-type Deconvolution	GenCompBio: General Computational Biology	Motivation: Cell-type deconvolution is a computational approach to infer cellular distributions from bulk transcriptomics data. Several methods have b [...]
24 July 14:00-14:20 (add to calendar)	01A	Yu-Hsiang Tseng	Ultrafast and Ultralarge Multiple Sequence Alignments using TWILIGHT	HiTSeq: High Throughput Sequencing Algorithms & Applications	Motivation: Multiple sequence alignment (MSA) is a fundamental operation in bioinformatics, yet existing MSA tools are struggling to keep up with the [...]
24 July 14:00-14:20 (add to calendar)	01B	Arnaud Belcour	Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data	MICROBIOME	Motivation: Taxonomic analysis of environmental microbial communities is now routinely performed thanks to advances in DNA sequencing. Determining the [...]
24 July 14:00-14:20 (add to calendar)	11BC	Yingying Wei	Detection of Cell-type-specific Differentially Methylated Regions in Epigenome-Wide Association Studies	RegSys: Regulatory and Systems Genomics	DNA methylation at cytosine-phosphate-guanine (CpG) sites is one of the most important epigenetic markers. Therefore, epidemiologists are interested i [...]
24 July 14:00-14:20 (add to calendar)	03B	Christophe Dessimoz	The missing link in FAIR data policy: data resources	Stewardship Critical Infrastructure	Over the past decade, the FAIR principles which provide guidance in making data Findable, Accessible, Interoperable, and Reusable have transformed the [...]
24 July 14:00-14:20 (add to calendar)	12	Caralyn Reisle	Human-AI Collaboration for Cancer Knowledge Verification: Insights from the CIViC-Fact Dataset	Text Mining: Text Mining for Healthcare and Biology	Interpretation of genomic findings remains one of the largest barriers to automation in processing precision oncology patient data due to the high lev [...]
24 July 14:00-16:00 (add to calendar)	11A		Defining principles for working together on training and skills development	WEB: Workshop on Education for Bioinformatics	This session will be split into two sections and will be run as a workshop gathering ideas and ways to move forward from the wider ISMB training commu [...]
24 July 14:00-14:40 (add to calendar)	02N	Yiliang Ding	Decoding RNA language in plants	iRNA: Integrative RNA Biology	RNA structure plays an important role in the post-transcriptional regulations of gene expression. Using in vivo RNA structure profiling methods, we ha [...]
24 July 14:20-14:40 (add to calendar)	01C	Steven Golob	Synthetic Data Generation for bulk RNA-seq Data: A CAMDA Health Challenge Analysis	CAMDA: Critical Assessment of Massive Data Analysis	One of the major barriers to AI-driven medical discoveries is the limited availability of high-quality, accessible healthcare data. This is because me [...]
24 July 14:20-14:40 (add to calendar)	03A	Osamu Muto	RVINN: A Flexible Modeling for Inferring Dynamic Transcriptional and Post-Transcriptional Regulation Using Physics-Informed Neural Networks	GenCompBio: General Computational Biology	Dynamic gene expression is controlled by transcriptional and post-transcriptional regulation. Recent studies on transcriptional bursting and buffering [...]
24 July 14:20-14:40 (add to calendar)	01A	Arseny Shur	GreedyMini: Generating low-density DNA minimizers	HiTSeq: High Throughput Sequencing Algorithms & Applications	Motivation: Minimizers are the most popular k-mer selection scheme in algorithms and data structures analyzing high-throughput sequencing (HTS) data. [...]
24 July 14:20-14:30 (add to calendar)	01B	Florian Plaza Oñate	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data	MICROBIOME	Metagenomic sequencing provides profound insights into microbial communities, but it is often compromised by technical biases, including cross-sample [...]
24 July 14:20-14:40 (add to calendar)	11BC	Weicai Long	MutBERT: Probabilistic Genome Representation Improves Genomics Foundation Models	RegSys: Regulatory and Systems Genomics	Motivation: Understanding the genomic foundation of human diversity and disease requires models that effectively capture sequence variation, such as s [...]
24 July 14:20-14:40 (add to calendar)	03B	Guy Cochrane	Sustaining global biodata: from resources to sustained infrastructure	Stewardship Critical Infrastructure	Just as scientific data are essential for life science and biomedical research, the databases, services and tools that enable scientists to safeguard, [...]
24 July 14:20-14:40 (add to calendar)	12	Tiffany Ta	Named entity recognition and relationship extraction to mine minimum inhibitory concentration of antibiotics from biomedical text	Text Mining: Text Mining for Healthcare and Biology	Antimicrobial resistance (AMR) poses a global public health threat, undermining modern medicine by diminishing the effectiveness of antibiotics for tr [...]
24 July 14:30-14:40 (add to calendar)	01B	Sebastien Raguideau	Longflow: A comprehensive end-to-end solution for long-read metagenomics.	MICROBIOME	Transitioning from short-read to long-read sequencing in metagenomics requires methodological refinements. We present Longflow, a versatile pipeline t [...]
24 July 14:40-15:40 (add to calendar)	04AB	Ingrid Hotz	Visual Data Analysis Research in Biomedical Applications: Navigating the Line Between Scientific Novelty and Practical Impact	BioVis: Biological Data Visualizations	Visualization has a long-standing tradition in biomedical research, yet its potential as a tool for data exploration and analytical reasoning remains [...]
24 July 14:40-15:00 (add to calendar)	01C	Patrick McKeever	Comparison of Single Cell RNA Synthetic Data Generators: A CAMDA Health Challenge Analysis	CAMDA: Critical Assessment of Massive Data Analysis	Single cell RNA sequencing has a wide range of applications in medical research, allowing researchers to identify distinct cell types and consider the [...]
24 July 14:40-15:00 (add to calendar)	01C	Jules Kreuer	NoisyDiffusion: Privacy Preserving Synthetic Gene Expression Data Generation	CAMDA: Critical Assessment of Massive Data Analysis	Generating synthetic gene expression data has the potential to advance computational biology and health research by enabling broader access to data. H [...]
24 July 14:40-15:00 (add to calendar)	03A	Robert Patton	A deep learning framework for predicting single gene expression from cell-free DNA	GenCompBio: General Computational Biology	Liquid biopsy derived circulating tumor DNA (ctDNA) profiling is increasingly used as a minimally invasive alternative to traditional biopsies. Epigen [...]
24 July 14:40-15:00 (add to calendar)	01A	Mehmet Alper Yilmaz	LYCEUM: Learning to call copy number variants on low coverage ancient genomes	HiTSeq: High Throughput Sequencing Algorithms & Applications	Motivation: Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contribu [...]
24 July 14:40-14:50 (add to calendar)	01B	Luis Pedro Coelho	Long-reads metagenome-assembled genomes can be higher quality than reference genomes: the case of the Shanghai pet dog microbiome catalog	MICROBIOME	We present a comprehensive analysis of the gut microbiome of 50 pet dogs living in Shanghai (China). Both long-read and short-read sequencing methods [...]
24 July 14:40-15:00 (add to calendar)	11BC	Abdul Muntakim Rafi	Detecting and avoiding homology-based data leakage in genome-trained sequence models	RegSys: Regulatory and Systems Genomics	Models that predict function from DNA sequence have become critical tools in deciphering the roles of genomic sequences and genetic variation within t [...]
24 July 14:40-15:00 (add to calendar)	03B	Susan Gregurick	NIH’s Strategic Vision for Data Science	Stewardship Critical Infrastructure
24 July 14:40-15:00 (add to calendar)	12	Chih-Hsuan Wei	Enhancing Biomedical Relation Extraction with Directionality	Text Mining: Text Mining for Healthcare and Biology	Biological relation networks contain rich information for understanding the biological mechanisms behind the relationship of entities such as genes, p [...]
24 July 14:40-15:00 (add to calendar)	02N	Baudouin Seguineau de Préval	The tangled dynamics of H/ACA snoRNAs to channel Pseudouridine Levels in the Human Ribosome	iRNA: Integrative RNA Biology	The human ribosome is densely decorated by 235—sometimes overlapping—modified nucleosides interspersing the 28S, 18S, and 5.8S ribosomal RNA (rRNA). T [...]
24 July 14:50-15:00 (add to calendar)	01B	Oleg Reva	Use of Long-Read SMRT PacBio Sequencing for Detailed Genomic and Epigenetic Studies of Complex Microbial Communities in the Wheat Rhizosphere to Abiotic Stress	MICROBIOME	The wheat rhizosphere harbours complex microbial communities essential for plant health and soil fertility. Traditional sequencing reveals microbial d [...]
24 July 15:00-15:20 (add to calendar)	01C	Serghei Mangul	Reusability of Public Omics Data Across 6 Million Publications	CAMDA: Critical Assessment of Massive Data Analysis	Over the past two decades, public repositories like GEO and SRA have accumulated vast omics datasets, sparking a crucial discussion on secondary data [...]
24 July 15:00-15:20 (add to calendar)	01C	Serghei Mangul	Pre-publication sharing of omics data improves paper citations	CAMDA: Critical Assessment of Massive Data Analysis	Advancements in omics technologies generate vast datasets, while public repositories facilitate their sharing, crucial for accelerating discovery, enh [...]
24 July 15:00-15:20 (add to calendar)	03A		MAGPIE: Multi-modal alignment of genes and peaks for integrated exploration of spatial transcriptomics and spatial metabolomics data	GenCompBio: General Computational Biology	Recent developments in spatially resolved -omics have enabled studies linking gene expression and metabolite levels to tissue morphology, offering new [...]
24 July 15:00-15:20 (add to calendar)	01A	Lucrezia Patruno	POPSICLE: a probabilistic method to capture uncertainty in single-cell copy-number calling	HiTSeq: High Throughput Sequencing Algorithms & Applications	During tumour evolution, cancer cells acquire somatic copy-number alterations (CNAs), that are frequent genomic alterations resulting in the amplifica [...]
24 July 15:00-15:10 (add to calendar)	01B	Anastasiia Grekova	proMGEflow: recombinase-based detection of mobile genetic elements in bacterial meta(genomes)	MICROBIOME	Mobile Genetic Elements (MGEs) are drivers of bacterial adaptation and can increase fitness of microbial communities in the changing environment. Yet [...]
24 July 15:00-15:20 (add to calendar)	11BC	Susanne Bornelöv	Predicting gene expression using millions of yeast promoters reveals cis-regulatory logic	RegSys: Regulatory and Systems Genomics	Gene expression is largely controlled by transcription factors and their binding and interactions in gene promoter regions. Early attempts to use deep [...]
24 July 15:00-15:20 (add to calendar)	03B	Phil Bourne	Your Science Needs You	Stewardship Critical Infrastructure	What can you do as a graduate student, postdoc, professor, leader to address the scientific moment we find ourselves in? We will come with a few sugge [...]
24 July 15:00-15:20 (add to calendar)	12	Daniela Gaio	Metadata extraction: Large Language Models (LLMs) to the rescue	Text Mining: Text Mining for Healthcare and Biology	In this project, our research group embarked on an extensive effort to download and re-analyze all globally and publicly accessible metagenomic sample [...]
24 July 15:00-15:20 (add to calendar)	02N	Hamed Najafabadi	Machine learning-guided isoform quantification in bulk and single-cell RNA-seq using joint short- and long-read modeling	iRNA: Integrative RNA Biology	Accurate quantification of transcript isoforms is crucial for understanding gene regulation, functional diversity, and cellular behavior. Existing RNA [...]
24 July 15:10-15:20 (add to calendar)	01B	Balazs Erdos	Extracting host-specific developmental signatures from longitudinal microbiome data	MICROBIOME	Longitudinal microbiome studies offer critical insights into microbial community dynamics, helping to distinguish true biological signals from interin [...]
24 July 15:20-15:40 (add to calendar)	01C	Yuexi Gu	HI-MGSyn: A Hypergraph and Interaction-aware Multi-Granularity Network for Predicting Synergistic Drug Combinations	CAMDA: Critical Assessment of Massive Data Analysis	Motivation: Drug combinations can not only enhance drug efficacy but also effectively reduce toxic side effects and mitigate drug resistance. With [...]
24 July 15:20-15:40 (add to calendar)	03A	Clemens Kohl	CAdir: Fast Clustering and Visualization of Single-Cell Transcriptomics Data by Direction in CA Space	GenCompBio: General Computational Biology	Clustering for single-cell RNA-seq aims at finding similar cells and grouping them into biologically meaningful clusters. Many available clustering al [...]
24 July 15:20-15:40 (add to calendar)	01A	Kendell Clement	MutSuite: A Toolkit for Simulating and Evaluating Mutations in Aligned Sequencing Reads	HiTSeq: High Throughput Sequencing Algorithms & Applications	Simulated sequencing reads containing known mutations are essential for developing, testing, and benchmarking mutation detection tools. Most existing [...]
24 July 15:20-15:30 (add to calendar)	01B	Gijs Selten	Complex SynCom inoculations to study root community assembly	MICROBIOME	The root microbiome is a complex system composed of millions of interacting microbes, some of which have plant-beneficial traits such as priming the p [...]
24 July 15:20-16:00 (add to calendar)	11BC	Luca Pinello	Learning the Regulatory Genome by Destruction and Creation	RegSys: Regulatory and Systems Genomics	The regulatory genome operates through a complex DNA language that controls gene expression. In this keynote, I will present two complementary approac [...]
24 July 15:20-16:00 (add to calendar)	03B		Open Discussion	Stewardship Critical Infrastructure
24 July 15:20-15:40 (add to calendar)	12	Shanfeng Zhu	Large-scale semantic indexing of Spanish biomedical literature using contrastive transfer learning	Text Mining: Text Mining for Healthcare and Biology	The exponential growth of biomedical literature has made automatic indexing essential for advancing biomedical research. While automatic indexing has [...]
24 July 15:20-15:40 (add to calendar)	02N	Yoshihisa Tanaka	Long-read RNA sequencing unveils a novel cryptic exon in MNAT1 along with its full-length transcript structure in TDP-43 proteinopathy	iRNA: Integrative RNA Biology	Understanding the role of transcript isoforms is crucial for dissecting disease mechanisms. TAR DNA binding protein-43 (TDP-43) is a key regulator of [...]
24 July 15:30-15:40 (add to calendar)	01B	Julia C Engelmann	Spatial and temporal variation of marine microbial interactions around the west Antarctic Peninsula	MICROBIOME	The west Antarctic Peninsula (WAP) has experienced more dramatic increases in temperature due to climate change than the rest of the continent and the [...]
24 July 15:40-16:00 (add to calendar)	01C		CAMDA Trophy	CAMDA: Critical Assessment of Massive Data Analysis
24 July 15:40-16:00 (add to calendar)	01C		Closing remarks	CAMDA: Critical Assessment of Massive Data Analysis
24 July 15:40-16:00 (add to calendar)	01A	Joao P. C. R. Mendonca	Landscape of The Dark Genome’s variants and their influence on cancer	HiTSeq: High Throughput Sequencing Algorithms & Applications	Human endogenous retroviruses (HERVs) are remnants of ancient viral infections that now make up ~8% of the human genome. Although typically silenced, [...]
24 July 15:40-15:50 (add to calendar)	01B	Tess Cherlin	Associations between Microbiome-Associated Variants and Diseases	MICROBIOME	High throughput sequencing, studies have investigated the microbiome’s association with diseases and genetic variants. We aimed to 1) extended previou [...]
24 July 15:40-16:00 (add to calendar)	12	Enio Gjerga	Reading papers: Extraction of molecular interaction networks with large language models	Text Mining: Text Mining for Healthcare and Biology	Motivation: Signalling occurs within and across cells and orchestrates essential cellular processes in complex tissues. Cell signalling involves sever [...]
24 July 15:40-15:50 (add to calendar)	02N	Tianyuan Liu	Transcriptome Universal Single-isoform COntrol (TUSCO): A Framework for Evaluating Transcriptome Quality	iRNA: Integrative RNA Biology	Long-read sequencing (LRS) platforms, such as Oxford Nanopore (ONT) and Pacific Biosciences (PacBio), enable comprehensive transcriptome analysis but [...]
24 July 15:50-16:00 (add to calendar)	01B	Witold Rudnicki	Detecting Synergistic Associations in Microbial Communities via Multi-Dimensional Feature Selection	MICROBIOME	The gut microbiome regulates host immunity, barrier function, and inflammatory processes. While many studies have identified individual taxa associate [...]
24 July 15:50-16:00 (add to calendar)	02N		Concluding remarks and poster prizes	iRNA: Integrative RNA Biology
24 July 16:20-18:00 (add to calendar)	01A	Fabian Theis	Decoding cellular systems: From observational atlases to generative interventions	Distinguished Keynotes	Over the past decade, the field of computational cell biology has undergone a transformation — from cataloging cell types to modeling how cells behave [...]
24 July 16:20-18:00 (add to calendar)	-	David Baker	A Conversation with Nobel Laureate David Baker: Inspiration from a Life in Science	Distinguished Keynotes	This special fireside chat features Nobel Laureate David Baker in a candid and inspiring conversation with Christine Orengo. Rather than exploring the [...]